| Accepted Posters |
| Category 'W'- Structure and Function Prediction' |
| Poster W001 |
| Linguistic Analysis of Unknown Metagenomic Sequences |
| Victor Seguritan- San Diego State University / Claremont Graduate University |
| No additional authors |
| Short Abstract: A method is needed to assign functions to unknown sequences which does not rely on sequence homology alone. The linguistic elements, syntax and semantics, of several model proteins will be used to assign functions to unknown metagenomes in a manner similar to the concept of understanding human language. |
| Long Abstract: Click Here |
| Poster W002 |
| From protein local structure prediction to local flexibility prediction: flexibility versus structural prediction errors. |
| Aurélie Bornot- INSERM UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot - Paris 7 |
| Catherine Etchebest (INSERM UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot - Paris 7, ); Alexandre G. de Brevern (INSERM UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot - Paris 7, ); |
| Short Abstract: In this study, we addressed the question of the structural “predictability” of a protein sequence with regards to its structural flexibility properties.Protein local structure dynamics were analyzed using X-ray experiments and molecular dynamics simulations. Finally, an original flexibility prediction method from protein sequence was proposed. |
| Long Abstract: Click Here |
| Poster W003 |
| Prediction of thermodynamic stability of transmembrane helices reveals architectural patterns of integral membrane proteins |
| Joke Reumers- Vrije Universiteit Brussel |
| Joost Schymkowitz (Vrije Universiteit Brussel, VIB Switch Laboratory); Frederic Rousseau (Vrije Universiteit Brussel, VIB Switch Laboratory); Luis Serrano (Centre for Genomic Regulation , Systems Biology Programme); |
| Short Abstract: With Casablanca we propose a statistical thermodynamics algorithm that predicts transmembrane helices based on simple structural assumptions and thus is able to distinguish structurally important helices from functional helices. We demonstrate the method is accurate on a large data set and can be used for genome wide screening. |
| Long Abstract: Click Here |
| Poster W004 |
| Sasichandran: A sequence specific dihedral angle database and evaluation tool |
| S. M. Minhaz Ud-Dean- University of Dhaka |
| MAHDI MOOSA (University of Dhaka, Genetic Engineering and Biotechnology); |
| Short Abstract: Estimation and prediction of dihedral angle can be used to validate both theoretically predicted and experimentally determined structures. This idea is used to develop a sequence specific dihedral angle prediction tool, Sasichandran. This tool can also evaluate a protein structure using information of sequence specific distribution of Ramachandran angles. |
| Long Abstract: Click Here |
| Poster W005 |
| Chemocavity: Specific Concavity in Protein Reserved for the Binding of Biologically Functional Small Molecules |
| Shinji Soga- Astellas Pharma Inc. |
| Hiroki Shirai (Astellas Pharma Inc., Molecular Medicine Research Laboratories, Drug Discovery Research); Masato Kobori (Astellas Pharma Inc., Molecular Medicine Research Laboratories, Drug Discovery Research); Noriaki Hirayama (Tokai University School of Medicine, Basic Medical Science and Molecular Medicine); |
| Short Abstract: Understanding what characteristics of the site determine the binding ability of a functional small molecule is not so easy. Here we introduced an index characterizing the binding site based on the concurrency rate of amino acid and identified a specific site on a protein for a particular functional small molecule. |
| Long Abstract: Click Here |
| Poster W006 |
| btmxMotif: A program to predict burial status motifs in transmembrane beta barrel strands based on expectation maximization |
| Sikander Hayat- Saarland University |
| No additional authors |
| Short Abstract: We employ expectation maximization as described in the MEME algorithm to discover motifs based on the predicted burial status of TM residues in Transmembrane beta-Barrel strands. The predicted burial status of TM residues is obtained using a statistical method named BTMX. |
| Long Abstract: Click Here |
| Poster W007 |
| Predicting protein function from domain content |
| Kristoffer Forslund- Stockholm Bioinformatics Centre |
| Erik Sonnhammer (Stockholm University, Stockholm Bioinformatics Centre); |
| Short Abstract: We present a framework for representing how sets of protein sequence domains give rise to protein function. This work extends previous approaches that map GO terms to Pfam domains by considering the functional implications of combinations of several domains. Probabilistic and rule-based models are evaluated and implemented as function predictors. |
| Long Abstract: Click Here |
| Poster W008 |
| Model Quality Assessment for Membrane Proteins |
| Sebastian Kelm- University of Oxford |
| Jiye Shi (UCB Group, ROC); Charlotte M. Deane (University of Oxford, Statistics); |
| Short Abstract: Membrane proteins are among the most important classes of drug targets, but experimentally obtaining their 3D structure is hard. Accuracte computational structure prediction is therefore of great value.With this aim in mind, we present a new suite of Model Quality Assessment Programmes for membrane proteins, which enable better model selection. |
| Long Abstract: Click Here |
| Poster W009 |
| Structure and evolution of protein allosteric sites |
| Alejandro Panjkovich- Institute of Biotechnology and Biomedicine, Universitat Autonoma de Barcelona |
| Xavier Daura (Catalan Institution for Research and Advanced Studies (ICREA), Institute of Biotechnology and Biomedicine (IBB), Universitat Autonoma de Barcelona); |
| Short Abstract: Protein ligand binding sites in general and allosteric sites in particular are of great interest, both in the applied context of drug development and in the academic understanding of allosterism. We performed a large-scale study on the evolution and structure of ligand binding sites, involving thousands of protein families. |
| Long Abstract: Click Here |
| Poster W010 |
| Relationships between the quality of homology models and the accuracy of ligand-protein docking results |
| Annalisa Bordogna- Universita' degli Studi di Milano - Bicocca |
| Alessandro Pandini (National Institute for Medical Research, London, Division of Mathematical Biology); Laura Bonati (Universita' degli Studi di Milano - Bicocca, DISAT); |
| Short Abstract: We investigated how the quality of homology models can affect the accuracy of ligand-docking experiments.Our results demonstrated that the quality of the modelled binding site, assessed by comparison to the native and the template protein structure, is an informative measure to predict the accuracy of the docking result. |
| Long Abstract: Click Here |
| Poster W011 |
| What kind of atoms are there? Natural atomic types from PDB and their relevance for structural modeling. |
| Enrico Pieroni- CRS4 |
| Maria Valentini (CRS4, Bioinformatics Lab); Detlef Walter Maria Hofmann (CRS4, Renewable Energy); |
| Short Abstract: We present a knowledge-based Force Field obtained by parsing PDB protein-ligand complexes to automatically identify natural atomic types and Force Field parameters. Advantages are: long range interactions automatically taken into account, interaction description relies only on natural interacting pairs, Hydrogen coordinates and partial charges calculations become obsolete. |
| Long Abstract: Click Here |
| Poster W012 |
| Computing Structures of Symmetric Homo-oligomeric Protein Complexes |
| Amarda Shehu- George Mason University |
| Christopher Miles (George Mason University, Computer Science); Amarda Shehu (George Mason University, Computer Science); |
| Short Abstract: We propose a method to compute symmetric homo-oligomeric protein structures assembled from a monomer of known semi-rigid structure. Geometric considerations rapidly extract candidatestructures from a protein complex database. Functional interfaces andphysico-chemical considerations further narrow predictions. The methodpresents a first step toward the design of large protein complexes. |
| Long Abstract: Click Here |
| Poster W013 |
| New Local Structure Properties for Creating Local Structure Alphabets |
| Grant Thiltgen- University of California, Santa Cruz |
| Kevin Karplus (University of California, Santa Cruz, Biomolecular Engineering); |
| Short Abstract: Combining local structure alphabets with sequence information has been shown to improve template searches. Our lab explores new structural features in order to create new alphabets. One feature is r_rot, and combining this feature with torsion angles and hydrogen bonds shows improvements over using these features alone. |
| Long Abstract: Click Here |
| Poster W014 |
| FREAD revisited: database search loop prediction |
| Yoonjoo Choi- Oxford University |
| No additional authors |
| Short Abstract: Over recent years, database search methods have been ignored. In light of the continued rapid expansion in the number of known protein structures we have re-evaluated FREAD, a database search method. In a direct comparison to MODELLER and other ab initio methods, FREAD is found to perform significantly better for an identifiable subset of loops. |
| Long Abstract: Click Here |
| Poster W015 |
| Structural rearrangement in the TCRpMHC formation in reaction to agonistic and antagonistic peptides |
| Bernhard Knapp- Medical University of Vienna |
| Wolfgang Schreiner (Medical University of Vienna, Biomedical Computersimulation and Bioinformatics); |
| Short Abstract: We present series of molecular dynamics simulations of two different TCRpMHC complexes. The first complex contains an agonistic peptide, the second an antagonistic one. The structural rearrangement in the CDRs of the TCRs in reaction to the different peptides is characterized. |
| Long Abstract: Click Here |
| Poster W016 |
| Comparison of proteins flexibilities by self-organizing maps: the test case of SH3 and its mutants |
| Domenico Fraccalvieri- Università degli Studi di Milano - Bicocca |
| Alessandro Pandini (National Institute for Medical Research, Division of Mathematical Biology); Fabio Stella (Università degli Studi di Milano - Bicocca, Dipartimento di Informatica Sistemistica e Comunicazione); Laura Bonati (Università degli Studi di Milano - Bicocca, Dipartimento di Scienze dell'Ambiente e del Territorio); |
| Short Abstract: A use of self-organizing maps in the analysis of molecular dynamics data is presented. The method was tested on a group of mutants of the SH3 domain and allowed to easily recover information about differences in the domain flexibilities that affect the biological function. |
| Long Abstract: Click Here |
| Poster W017 |
| Cryo-EM study and 3-D Structure determination of pore forming toxin |
| Somnath Dutta- National Institute of Cholera nad Enteric Diseases |
| No additional authors |
| Short Abstract: Mature Pore Forming Toxin (PFT) is 100-times more effective than truncated PFT. 3D structure of both types of PFTS is determined using cryo-EM and single particle analysis technique. Docking was also performed and 3D structure was observed using CHIMERA. Good structural differences explain the less pore formation activity and also explain pore formation mechanism. |
| Long Abstract: Click Here |
| Poster W018 |
| Modeling protein motions and ordering NMR models with the help of mass transportation theory |
| Sergey Nikolenko- Steklov Mathematical Institute |
| Eugene Stepanov (St. Petersburg State University of Information Technology, Mechanics & Optics, IT); Monica Zoppè (Institute of Clinical Physiology, National Research Council, Pisa, Italy, Laboratory of Molecular Biology); Yury Porozov (Institute of Clinical Physiology, National Research Council, Pisa, Italy, Laboratory of Molecular Biology); |
| Short Abstract: Knowledge about motion is crucial for understanding the proteins' functions. It is possible to reconstruct a sequence of conformations defining a motion on the basis of NMR data. To solve the problem of ordering different conformations we use a mathematical model based on evaluation of cost of mass transfer during conformational transition. |
| Long Abstract: Click Here |
| Poster W019 |
| Annotating Functional Residues of the Melanocortin-4 Receptor |
| Yana Bromberg- Columbia University |
| Burkhard Rost (Columbia University, Biochemistry and Molecular Biophysics); |
| Short Abstract: Using the example of the human melanocortin-4 receptor, we present a novel approach to prediction of functionally important residues from sequence. We computationally quantify functional consequences of all possible substitutions at each sequence position and compile per-residue importance scores. Our predictions correlate well with known functional sites. |
| Long Abstract: Click Here |
| Poster W020 |
| A density based approach to define structural alphabets |
| Alessandro Pandini- National Institute for Medical Research |
| Jens Kleinjung (National Institute for Medical Research, Division of Mathematical Biology); |
| Short Abstract: We present a new approach to extract representative fragments that are attractors in protein structure space. Highly populated attractors are also expected to be the most energetically stable conformations.The density based structural alphabets are both optimal to reconstruct known proteins and informative to describe the most favourable conformations. |
| Long Abstract: Click Here |
| Poster W021 |
| Visualization and modeling of protein motion. Autodesk Maya as a reliable and fast instrument for macromolecular dynamic representation. |
| Yuri Porozov- Insitute of Clinical Physiology. CNR |
| Raluca Andrei (Scuola Normale Superiore, Lab of Molecular Biology); Monica Zoppe' (Scientific Visualization Unit, Inst. of Clinical Physiology CNR); |
| Short Abstract: An approach for dynamic modeling of protein behavior based on 3D animation software and artificial implementation of forces influencing protein motion is presented. Evaluation of the method using NMR models of Calcium-free Calmodulin shows that it is possible to use it as powerful tool for protein visualization and motion prediction. |
| Long Abstract: Click Here |
| Poster W022 |
| SitesIdentify: Prediction of functional sites on the surface of proteins |
| Tracey Bray- The University of Manchester |
| Pedro Chan (The University of Manchester, Faculty of Life Sciences); Richard Greaves (The University of Manchester, Faculty of Life Sciences); Salim Bougouffa (The University of Manchester, Faculty of Life Sciences); Andrew Doig (The University of Manchester, Manchester Interdisciplinary Biocentre); Jim Warwicker (The University of Manchester, Faculty of Life Sciences); |
| Short Abstract: We present a functional site prediction tool, SitesIdentify, which predicts the location of a functional site on the surface of a protein. We have compared our results to other publicly available tools and have provided our method via a web server at www.manchester.ac.uk/bioinformatics/sitesidentify |
| Long Abstract: Click Here |
| Poster W023 |
| The Extended RNAMute and its Applications |
| Alexander Churkin- Ben Gurion University of the Negev |
| Danny Barash (Ben Gurion University of the Negev, Department of Computer Science); |
| Short Abstract: RNAMute is a bioinformatics application that aims to solve the RNA mutation predictionproblem. Given an RNA sequence, the goal is to compute the minimal number of mutations required to disrupt important secondary structure motifs. The extended RNAMute offers an advanced way to perform efficient and reliable mutation predictions. |
| Long Abstract: Click Here |
| Poster W024 |
| Using multi-data hidden Markov models trained on local neigh-borhoods of protein structure to predict residue-residue contacts |
| Patrik Björkholm- Stockholm Bioinformatics Center |
| No additional authors |
| Short Abstract: We propose a novel hidden Markov model based method for predicting residue-residue contacts from protein sequences using as training data homologous sequences, predicted secondary structure and a library of local neighborhoods (local descriptors of protein structure). The library consists of recurring structural entities in-corporating short-, medium- and long-range interactions. |
| Long Abstract: Click Here |
| Poster W025 |
| A Quantitative Pan-Receptor Predictive Method for Peptide Recognized by the SH2 Domain Family |
| Hao Zhang- Technical University of Denmark |
| No additional authors |
| Short Abstract: Src-homology 2 (SH2) domain is the largest class of known phosphotyrosine recognition structures. Characterization of the binding specificity is of pivotal importance. The challenge for both experimental and computational approaches is its large genetic diversity. We present a neural network method that leverages information from neighbouring receptors to unknowns. |
| Long Abstract: Click Here |
| Poster W026 |
| The Restricted Protein Redesign Problem: Efficient Search via Restricted Dead-End Elimination |
| Maria Safi- University of Toronto |
| No additional authors |
| Short Abstract: Dead-End Elimination (DEE) has emerged as a powerful conformational search technique enabling structure-based, computational protein redesign. We present rDEE as the solution of choice, when the desired number of mutations k is less than the number of mutable residues n. |
| Long Abstract: Click Here |
| Poster W027 |
| Protein folding -- from start to finish |
| Jonathan Ellis- Macquarie university |
| Fabian Huard (Macquarie university, Statistics); Charlotte Deane (Oxford university, Statistics); Graham Wood (Macquarie university, Statistics); |
| Short Abstract: Cotranslational folding may confer benefits to protein folding; such ashelping the peptide avoid kinetic traps. These benefits areinvestigated on proteins displaying both signs of cotranslationalfolding and post-translational folding. At times, sequential foldingperforms better than non-sequential. This suggests incorporation ofsequential folding may lead to better predictions. |
| Long Abstract: Click Here |
| Poster W028 |
| MOLECULAR DYNAMIC SIMULATION TO MONILIPHOTHORA PERNICIOSA CHITINASE, THE AGENT OF WITCHES’ BROOM DISEASE ON THEOBROMA CACAO |
| Rafaela Galante- University of Feira de Santana. |
| Catiane Souza (State University of Feira de Santana, Biological Science); Bruno Andrade (State University of Feira de Santana, Biological Science); Sandra Assis (State University of Feira de Santana, Health Science); Julio Carcardo (State University of Santa Cruz, Biological Science); Aristóteles Góes-Neto (State University of Feira de Santana, Biological Science); Alex Taranto (State University of Feira de Santana, Health Science); |
| Short Abstract: Chitinases are released by M. perniciosa promoting hydrolysis of chitin, which is important to the development of the pathogen in Theobroma cacao. We constructed and refined the 3D structure of the chitinase of M. perniciosa. The quality of resultant model was evaluated by PROCHECK 3.0 and ANOLEA. |
| Long Abstract: Click Here |
| Poster W029 |
| GOdot in 2009 |
| Ingolf Sommer- Max-Planck-Institue for Informatics |
| Frederik Gwinner (Max-Planck-Institute for Informatics, Computational Biology); Anne-Christin Hauschild (Max-Planck-Institute for Informatics, Computational Biology); Aaron Weimann (Max-Planck-Institute for Informatics, Computational Biology); Thomas Lengauer (Max-Planck-Institute for Informatics, Computational Biology); |
| Short Abstract: The previously published GOdot system allows for predicting molecular functions of query proteins with known structure. The system assesses structural similarities of reference proteins and relates those to molecular function. Here, we present an incorporated visualization of the structural and functional neighborhood of proteins. Additionally, we present an update now using current reference structures. |
| Long Abstract: Click Here |
| Poster W030 |
| A new method to predict 3D structure for protein loops |
| Christelle Reynes- Université Paris Diderot |
| Anne-Claude Camproux (Université Paris Diderot, UFR SdV - Unité MTi); Robert Sabatier (Faculté de Pharmacie de Montpellier, Laboratoire de Physique Industrielle et Traitement de l'Information); Leslie Regad (University of Helsinky, Faculty of Pharmacy, Centre for Drug Research, Computational Drug Discovery group P.O.); |
| Short Abstract: Predicting 3D protein structures from amino acid sequences and especially in loops is addressed. After prior encoding of structure via structural letters, the proposed method firstly predicts single letters from amino-acids via genetic programming, then prediction is refined by a hidden Markov-model considering links between letters (transitions and confusions). |
| Long Abstract: Click Here |
| Poster W031 |
| Improving 3D model selection of membrane proteins |
| Arjun Ray- Center for Biomembrane Research |
| Bjorn Wallner (Center for Biomembrane Research, Dept. Biochemistry Bjorn); |
| Short Abstract: The huge gap between the number of membrane proteins in the genome (25%) and the membrane proteins in the structural database (less than 1%) makes it an ideal target for computational approaches. We have improved and extended ProQ, for model quality assessment of water soluble proteins, to membrane proteins. |
| Long Abstract: Click Here |
| Poster W032 |
| Changing the traditional picture of alpha-helical membrane proteins |
| Kristoffer Illergård- Stockholm University |
| Anni Kauko (Stockholm University, Department of Biochemistry and Biophysics); Arne Elofsson (Stockholm University, Department of Biochemistry and Biophysics); |
| Short Abstract: We have investigated unexpected regions such as coils, reentrant regions and polar residues in the middle of alpha-helical membrane proteins of known structures. The studies revealed interesting clues about the structure, function, folding and evolution of these proteins. |
| Long Abstract: Click Here |
| Poster W033 |
| Investigation and prediction of the severity of p53 mutants using parameters from structural calculations |
| Jonas Carlsson- Linköping University |
| Thierry Soussi (Karolinska Institutet, Oncology-Pathology, Cancer Center Karolinska (CCK)); Bengt Persson (Linköping University, IFM Bioinformatics); |
| Short Abstract: A method has been developed to predict effects of mutations in the p53 cancer suppressor gene, combining novel and previously established parameters. Each mutant is classified as deleterious or non-deleterious based on a severity score. The method has a prediction accuracy of 77%, which is better than earlier methods. |
| Long Abstract: Click Here |
| Poster W034 |
| Importance of local model quality for Molecular Replacement |
| Marcin Pawlowski- International Institute of Molecular and Cell Biology in Warsaw |
| No additional authors |
| Short Abstract: Computational models of protein structure have been shown to be useful as search models in Molecular Replacement. Our study shows that theoretical modeling in combination with accurate prediction of quality of models by MQAP can provide useful search models for crystallographic structure solution by MR. |
| Long Abstract: Click Here |
| Poster W035 |
| Prediction of causative effects of disease-related mutations at the molecular level by integrated bioinformatic analyses. |
| Jan Kosinski- International Institute of Molecular and Cell Biology |
| Bujnicki Janusz (International Institute of Molecular and Cell Biology, Laboratory of Bioinformatics and Protein Engineering); |
| Short Abstract: We present an integrated approach to predict the effects of missense mutations by mapping the functional sites using a broad spectrum of bioinformatic methods, such as sequence and structural analyses, modeling and docking. Our approach can be easily applied by biologists and serve as a guide for selecting appropriate tools. |
| Long Abstract: Click Here |
| Poster W036 |
| Fold recognition insights into function of two myeloid specific regulators of apoptosis - HAX1 and MLF1/MLF2 |
| Katarzyna Kokoszynska- Sklodowska-Curie Memorial Cancer Center and Institute of Oncology |
| No additional authors |
| Short Abstract: Here we present the results of fold recognition and identification of distant homology of two myeloid regulators of apoptosis – HAX1 and myeloid leukemia factors (MLF). We summarized the involvement of HAX1 proteins in calcium homeostasis and the current state of the knowledge on the function of HAX1/MFL families. |
| Long Abstract: Click Here |
| Poster W037 |
| Classification of the SDR Superfamily of Short-Chain Dehydrogenases/Reductases Using Hidden Markov Models |
| Yvonne Kallberg- Linköping Univ. & Karolinska Inst. |
| Fredrik Lysholm (Linkoping University, IFM Bioinformatics); Udo Oppermann (University of Oxford, 3Structural Genomics Consortium, The Botnar Research Centre, ); Bengt Persson (Linkoping University, IFM Bioinformatics); |
| Short Abstract: The largest dehydrogenase superfamily is SDR of short-chain dehydrogenases/reductases with presently ~47.000 members. It shows considerable divergence and there is a great need for sub-classification. We have now developed a family classification system and an accompanying nomenclature scheme that provide a systematic overview and allows for functional conclusions. |
| Long Abstract: Click Here |
| Poster W038 |
| Solvent in protein-protein interactions and its impact on protein contacts prediction |
| Sergey Samsonov- Biotec TU Dresden |
| Joan Teyra (BIOTEC TU Dresden, Structural Bioinformatics); Gerd Anders (BIOTEC TU Dresden, Structural Bioinformatics); M. Teresa Pisabarro (BIOTEC TU Dresden, Structural Bioinformatics); |
| Short Abstract: Although solvent is important in protein interfaces, its impact on protein-protein interactions in computational studies is often ignored. We analyze water-mediated interactions in protein interfaces by a MD approach and, in addition, demonstrate that introduction of solvent into the correlated mutations concept improves to a certain extent protein contacts predictions. |
| Long Abstract: Click Here |
| Poster W039 |
| Characterisation of novel proteins involved in mitosis by structure-based computational methods |
| Sontheimer Jana- BIOTEC TU Dresden |
| Mirko Theis (Max Planck Institute of Cell Biology and Genetics, Dresden); Frank Buchholz (Max Planck Institute of Cell Biology and Genetics, Dresden ); Maria Teresa Pisabarro (BIOTEC TU Dresden, Structural Bioinformatics); |
| Short Abstract: With full sequenced genomes, computational methods are gaining importance in characterisation of novel proteins. We have developed a framework for automatic structure-based function annotation and used it for analysing phenotypic data from genome-wide RNAi screenings, which has resulted in characterisation of a novel mitotic protein regarding its structure and function. |
| Long Abstract: Click Here |
| Poster W040 |
| Discovery of novel chemokines with automated structure-based functional protein annotation methods |
| Aurelie Tomczak- BIOTEC - Technical University Dresden |
| Maria Teresa Pisabarro (BIOTEC - Technical University Dresden, Structural Bioinformatics); |
| Short Abstract: We developed an automatic framework for structure-based annotation of proteins and use it to identify novel chemokines, which are proteins essential for guiding immune cell migration. We integrate publicly available sequence and structure information and feature prediction tools with fold recognition and identified promising candidates that are currently experimentally validated. |
| Long Abstract: Click Here |
| Poster W041 |
| Fast structural alignment of RNA using n-grams |
| Kristian Rother- International Institute of Molecular and Cell Biology in Warsaw |
| Raphael Bauer (Charite Medical University, Arnimallee 22, 14195 Berlin, Structural Bioinformatics Group); Marcus Schroeder (Charite Medical University, Arnimallee 22, 14195 Berlin, Structural Bioinformatics Group); Robert Preissner (Charite Medical University, Arnimallee 22, 14195 Berlin, Structural Bioinformatics Group); Janusz M. Bujnicki (International Institute of Molecular and Cell Biology in Warsaw, Bioinformatics and Protein Engineering Lab); |
| Short Abstract: We have created LaJolla, a structural alignment method for RNA. It represents the RNA backbone as strings, and uses N-grams for searching. We have benchmarked the method against SARA, and show improvements in the assignment of RNA function. |
| Long Abstract: Click Here |
| Poster W042 |
| Blender for biology: Game Engine for molecular animation and special effects for chemical and physical behavior |
| Monica Zoppè- Scientific Visualization Unit - LTGM |
| Raluca Andrei (Scuola Normale Superiore, Lab of Molecular Biology); Marco Callieri (CNR , ISTI); Tiziana Loni (BigBang Solutions, Graphics development); Maria Francesca Zini (CNR, Inst. of Clinical Physiology); Monica Zoppe' (CNR, Inst. of Clinical Physiology); |
| Short Abstract: We present an animation system based on the 3D open-source software Blender applied to the transition between two conformations of Calmodulin. Results are compatible with experimental data, and are visualized using a technique that reveals chemical and physical features immediately. The instrument is useful in research and other settings. |
| Long Abstract: Click Here |
| Poster W043 |
| Co-evolution of blocks of residues and sectors in protein structures |
| Linda Dib- CNRS-UPMC |
| Alessandra Carbone (CNRS-UPMC, Informatique); |
| Short Abstract: Evolutionarily conserved networks of residues have been demonstrated to mediate allosteric communication in proteins involved in cellular signaling. We propose a method to detect co-evolved blocks of residues, numerically rank them depending on their level of co-evolution, and clusterize them to obtain networks of co-evolved blocks. |
| Long Abstract: Click Here |
| Poster W044 |
| ModeRNA: A New Software Tool For Comparative Modeling of RNA 3D-Structures |
| Janusz Bujnicki- Intl. Institute of Molecular and Cell Biology (IIMCB) |
| Magdalena Musielak (Adam Mickiewicz University, PL-61-614 Poznan, Poland, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology); Tomasz Puton (Adam Mickiewicz University, PL-61-614 Poznan, Poland, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology); Kristian Rother (Intl. Institute of Molecular and Cell Biology (IIMCB), 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering); |
| Short Abstract: We are developing ModeRNA, a computer program for comparative RNA modeling. With this tool a user can obtain a 3D model of a target RNA molecule based on a homologous template structure from the PDB, and a target-template alignment of RNA sequences, by introducing nucleoside substitutions and insertions/deletions. |
| Long Abstract: Click Here |
| Poster W045 |
| A comparative study for definition and search of protein motifs |
| Annika Kreuchwig- Free University Berlin |
| Ina Koch ([1] TFH Berlin FB VI, Seestr. 64, 13347 Berlin / [2] Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, [1] Bioinformatics / [2] Computational Molecular Biology); Patrick May (Max Planck Institute for Molecular Plant Physiology Am Muehlenberg 1, 14476 Potsdam-Golm, Bioinformatics Group / GoFORSYS); |
| Short Abstract: Protein Topology Graph Library provides graph-theoretical descriptions of proteins. We define functional protein domains of protein topology graphs and introduce a new method to browse the database for topological protein structure motifs by pre-defined search patterns of structural motifs. We perform a comparative analysis with CATH, SCOP and TOPS. |
| Long Abstract: Click Here |
| Poster W046 |
| InterProScan New and Planned Developments |
| Manjula Thimma- European Bioinformatics Institute |
| Sarah Hunter (EBI, InterPro Team); Antony Quinn (EBI, Interpro Team); Phil Jones (EBI, InterProTeam); |
| Short Abstract: The InterPro database integrates multiple protein signature databases and provides a portal for protein functional and structural annotation. InterProScan is a software package which wraps the search algorithms for these signature databases into a single tool. This poster will present significant new developments in InterProScan. |
| Long Abstract: Click Here |
| Poster W047 |
| A geometric knowledge-based coarse-grained scoring potential for structure prediction evaluation |
| Sebastien LORIOT- INRIA |
| Frédéric Cazals (INRIA, ABS); Michael Levitt (Stanford University, Structural Biology); Julie Bernauer (INRIA, ABS); |
| Short Abstract: We present a method to derive multi-body contact potentials,based on the arrangement of circles on sphere.Using this geometric construction on coarse-grained protein models, we show thatwe can build various knowledge-based potentials, encoding up to 5-body contacts,able to distinguish native structures from decoys. |
| Long Abstract: Click Here |
| Poster W048 |
| firestar -predicting functional residues, new developements |
| Gonzalo Lopez- Cnio |
| Michael Tress (CNIO, Structural and Computational Biology Programm); Alfonso Valencia (CNIO, Structural and Computational Biology Programm); |
| Short Abstract: The prediction of functional residues with firestar is now wholly automated and has been made available as a web service. As part of the automatization of firestar we have linked functional residue predictions with GO molecular function terms and all binding sites are now filtered for biological relevance. |
| Long Abstract: Click Here |
| Poster W049 |
| PET(co)fold: Unification of evolutionary and thermodynamic information for RNA folding |
| Stefan Seemann- IBHV, University Of Copenhagen |
| Andreas S Richter (Inst. of Computer Science, Albert-Ludwigs-Univ. Freiburg, Chair for Bioinformatics); Rolf Backofen (Inst. of Computer Science, Albert-Ludwigs-Univ. Freiburg, Chair for Bioinformatics); Jan Gorodkin (IBHV, University Of Copenhagen, Genetics And Bioinformatics); |
| Short Abstract: PETfold has shown that the prediction of RNA structure in multiple aligned sequences can benefit from the unification of probabilistic evolutionary and thermodynamic model into a single optimization problem. In PETcofold, we extend the concept to search for RNA duplexes considering covariance and pseudoknots between intra- and intermolecular base pairs. |
| Long Abstract: Click Here |
| Poster W050 |
| Allostery Hotspot Prediction Using Support-vector Machines |
| Omar Demerdash- University of Wisconsin-Madison |
| Julie Mitchell (University of Wisconsin-Madison, Biochemistry and Mathematics); Michael Daily (University of Wisconsin-Madison, Chemistry); |
| Short Abstract: Allostery is the process whereby a ligand or protein-binding event at one site changes the activity at a distant site. Identifying residues that relay the signal between sites remains a challenge. We have developed a family of knowledge-based models using support vector machines for accurate prediction of allosteric “hot spots.” |
| Long Abstract: Click Here |
| Poster W051 |
| Predicting Protein Interface Residues from Functional Specificity |
| K. Anton Feenstra- Free University Amsterdam |
| Bas Dutilh (Radboud University Nijmegen, CMBI); Vera van Noort (Radboud University Nijmegen, CMBI); Martijn Huynen (Radboud University Nijmegen, CMBI); Giacomo Bastianelli (Institut Pasteur, Paris); Jaap Heringa (Free University Amsterdam, IBIVU/Computer Science); |
| Short Abstract: Functional specialization within protein families implies differences in protein-protein interactions. We select sub-type specific sites by comparing interacting orthologs with non-interacting paralogs using Sequence Harmony [NAR 35:W495; NAR 34:6540]. Selections are highly enriched in surface residues, and enriched in interface residues from known (PDB) complex structures. |
| Long Abstract: Click Here |
| Poster W052 |
| Evolutionarily driven algorithm for the quantification of protein patterns' similarity |
| Konstantinos Exarchos- Unit of Medical Technology & Intelligent Information Systems |
| George Rigas (Unit of Medical Technology & Intelligent Information Systems, Dept of Computer Science, University of Ioannina); Dimitrios Fotiadis (Unit of Medical Technology & Intelligent Information Systems, Dept of Computer Science, University of Ioannina); |
| Short Abstract: We propose an evolutionarily-driven algorithm which quantifies the statistical similarity between two patterns. The algorithm computes the Kullback-Leibler divergence, employing the residues’ substitution probabilities and their prior distribution. Thus, we determine whether a pattern is novel and consequently identify its functional propensity, by comparing it against the PROSITE database. http://sites.google.com/site/patterncomparer/. |
| Long Abstract: Click Here |
| Poster W053 |
| Model-structure, mutagenesis and functional characteristics of the NHA2 transporter |
| Maya Schushan- Tel-aviv university |
| Nir Ben-Tal (Prof. , Biochemistry); Minghui Xiang (Dr., Physiology); Rajini Rao (Dr., Physiology); Etana Padan (Prof., Molecular Microbial Ecology); |
| Short Abstract: We generated a model-structure of a novel human cation/proton transmembrane antiporter, NHA2, via a composite homology modeling approach. The model-structure is supported by evolutionary conservation analysis and guided mutagenesis experiments. Additionally, the model of NHA2 reveals some unique functional features, distinct from those of other family members. |
| Long Abstract: Click Here |
| Poster W054 |
| TESE: Generating specific protein structure test set ensembles |
| Silvio Tosatto- University of Padova |
| Francesco Sirocco (University of Padova, Dept. of Biology); |
| Short Abstract: TESE is a web server for the generation of test sets of protein sequences and structures fulfilling a number of different criteria. Structure classification is used to control structural/sequence redundancy and to interactively select protein subsets with specific characteristics. The TESE server is available for non-commercial use at URL: http://protein.bio.unipd.it/tese/. |
| Long Abstract: Click Here |
| Poster W055 |
| Comparative modeling of the SmSERCA protein of Schistosoma mansoni |
| Nelson Gichora- ILRI |
| Anna Tramontano (University of Rome "La Sapienza", Biochemical Sciences); |
| Short Abstract: We present our results having modeled the structure of Schistosoma mansoni SERCA (SmSERCA) protein by homology and compared using Modeller. The results will be used in the design of a specific drug that targets the artemisone binding site of the SmSERCA protein in the platyhelminth. |
| Long Abstract: Click Here |
| Poster W056 |
| GOPHER - An automatic server for function prediction evaluation |
| Jose Maria Fernandez- Spanish National Cancer Research Center (CNIO) |
| Angela del Pozo (Spanish National Cancer Research Center (CNIO), Structural and Computational Biology Programme); Gonzalo Lopez (Spanish National Cancer Research Center (CNIO), Structural and Computational Biology Programme); Michael Tress (Spanish National Cancer Research Center (CNIO), Structural and Computational Biology Programme); Alfonso Valencia (Spanish National Cancer Research Center (CNIO), Structural and Computational Biology Programme); Mark Wass (Imperial College London, Structural Bioinformatics Group); Michael Sternberg (Imperial College London, Structural Bioinformatics Group); |
| Short Abstract: We have developed a server, GOPHER, to assess protein function prediction in a continuous fashion. Predictors assign GO terms to weekly PDB updates and are assessed using a range of methods. The server is now functioning and we would like to invite developers to take part in this rolling assessment. |
| Long Abstract: Click Here |
| Poster W057 |
| WRAPPA: a Web-based Residue Analysis Program for Phobicity Assessment |
| Christopher Fraser- Institute for Mathematics and its Applications (IMA) |
| Thuong Van Du Tran (l’ ́Ecole Polytechnique `a Palaiseau, Laboratoire d’Informatique); Ariel Fernandez (Rice University, Bioengineering); L. Ridgway Scott (University of Chicago, Computer Science); |
| Short Abstract: Defectively packed hydrogen bonds, or “dehydrons”, play a significant role in protein-ligand interactions through the thermodynamically favorable exclusion of water. We introduce and validate a new bioinformatics application that screens for dehydrons within protein structures: a Web-Based Residue Analysis Program for Phobicity Assessment (WRAPPA). |
| Long Abstract: Click Here |
| Poster W058 |
| GOmotif: A web server for investigating the biological role of protein sequence patterns |
| Franklin Bristow- Public Health Agency of Canada |
| Runtao He (Public Health Agency of Canada, National Microbiology Laboratory); Gary Van Domselaar (Public Health Agency of Canada, National Microbiology Laboratory, Bioinformatics Core Facility); |
| Short Abstract: Biologically relevant sequence patterns (motifs) are commonly found in proteins. Experimentally ascertaining the biological relevance of novel motifs can be an expensive and time consuming process. GOmotif is a web based tool that searches Gene Ontology annotated protein databases to assist scientists in assigning biological roles to a novel motif. |
| Long Abstract: Click Here |
| Poster W059 |
| Prediction of Protein Binding Regions in Disordered Proteins |
| Balint Meszaros- Institute of Enzymology |
| Istvan Simon (Institute of Enzymology, Protein structure); Zsuzsanna Dosztanyi (Institute of Enzymology, Protein structure); |
| Short Abstract: Intrinsically unstructured/disordered proteins (IUPs/IDPs) do notadopt a stable structure in isolation but exist as highly flexibleconformational ensembles. Many IDPs function via binding to astructured partner and undergo a disorder-to-order transition. In thiswork we report a prediction method for such disordered bindingregions. |
| Long Abstract: Click Here |
| Poster W060 |
| Fragment-based replica-exchange method with adaptive parameter tuning |
| Masaaki Suzuki- The University of Tokyo |
| Hiroshi Okuda (The University of Tokyo, Research into Artifacts, Center for Engineering (RACE)); |
| Short Abstract: Fragment-based replica-exchange method (REM) with automatic parameter tuning has been developed. In the parameter tuning scheme, fragment length is optimized adaptively. Performing peptide folding simulations, we have found that the proposed REM successfully provides appropriate fragment length, and thus, good conformational sampling performance. |
| Long Abstract: Click Here |
| Poster W061 |
| Guidelines for fragment selection in protein structure prediction |
| Sheenal Srivastava- Macquarie University |
| Graham Wood (Macquarie University, Statistics); Jonathan Ellis (Macquarie University, Statistics); Charlotte Deane (Oxford University, Statistics); |
| Short Abstract: Fragment-based assembly methods are commonly employed to predict protein structure. We present a study of Rosetta fragment libraries and a first principles approach to better select fragments, based on a locational bias of the target protein sequence. |
| Long Abstract: Click Here |
| Poster W062 |
| Assessing conformational diversity in proteins using evolutionary information |
| Nicolas Palopoli- Universidad Nacional de Quilmes |
| Ezequiel Juritz (Universidad Nacional de Quilmes, Centro de Estudios e Investigaciones); Sebastian Fernandez Alberti (Universidad Nacional de Quilmes, Centro de Estudios e Investigaciones); Gustavo Parisi (Universidad Nacional de Quilmes, Centro de Estudios e Investigaciones); |
| Short Abstract: We have previously presented a method for 3D protein models discrimination based on evolutionary information. Here we show that our method is able to describe the conformational diversity of a protein, allowing us to select native-like models representing the conformational ensemble that characterizes the native state of the protein. |
| Long Abstract: Click Here |
| Poster W063 |
| How good can Template-based Modelling be? |
| Braddon Lance- Macquarie University |
| Graham Wood (Macquarie University, Department of Statistics); Charlotte Deane (Oxford University, Statistics); |
| Short Abstract: To predict the structure of a protein, the amino-acid sequence may be aligned with a related structure, and the prediction built from the corresponding fragments. We show how this prediction would be improved if the structure fragments were optimally positioned, and model this improvement as a function of protein properties. |
| Long Abstract: Click Here |
| Poster W064 |
| Automated scaffold selection in enzyme design |
| Christoph Malisi- Max Planck Institute for developmental biology |
| Birte Höcker (Max Planck Institute for developmental biology, Junior Research Group); Oliver Kohlbacher (Eberhard Karls University Tübingen, Computer Science); |
| Short Abstract: We present ScaffoldSelection, an algorithm for identifying attachment sites for catalytic motifs in protein structures. It identifies pairs of geometrically suitable backbone positions, and combines these with a graph clique search to complete attachment sites. ScaffoldSelection performed well in a benchmark involving the identification and geometric recapitulation of catalytic motifs in a large structure database. |
| Long Abstract: Click Here |
| Poster W065 |
| Compensatory patterns of tRNA recognition regions are preserved between bacterial and mitochondrial amino-acyl tRNA synthetases |
| Milana Morgenstern- Weizmann Institute of Science |
| Liron Klipcan (Weizmann Institute of Science, Structural Biology); Dmitry Tworowski (Weizmann Institute of Science, Structural Biology); Mark Safro (Weizmann Institute of Science, Structural Biology); |
| Short Abstract: We studied aminoacyl-tRNA synthetases (aaRSs), and their adaptation using correlated mutations. For eight bacterial aaRS-tRNA complexes and two mitochondrial aaRS, we found the 1.75-fold increase of mutations frequency in tRNA recognition regions. The compensatory patterns are preserved for tRNA recognition regions between corresponding bacterial and mitochondrial aaRSs. |
| Long Abstract: Click Here |
| Poster W066 |
| Data Mining of Enzymes using Specific Peptides |
| David Horn- Tel Aviv University |
| Uri Weingart (Tel Aviv University, Physics); Yair Lavi (Tel Aviv University, Physics); |
| Short Abstract: Employing Specific Peptides (SPs, Kunik et al 2007), motifs specific to branches of the EC classification hierarchy, we classify proteins into enzyme categories. Very good results are obtained both on positive and negative data. The method is applied to several metagenomic datasets, whose enzymatic profiles are predicted. |
| Long Abstract: Click Here |
| Poster W067 |
| FiberDock: Modeling Restricted Backbone Flexibility in Docking |
| Efrat Mashiach- Tel-Aviv University |
| Ruth Nussinov (National Cancer Institute, Center for Cancer Research Nanobiology Program); Haim J. Wolfson (Tel Aviv University, School of Computer Science); |
| Short Abstract: FiberDock is a novel docking refinement method that models backbone and side-chain flexibility. The method minimizes backbone conformations along the most relevant normal modes, which correlate with chemical forces. It uses both low and high frequency modes and therefore is able to model global and local conformational changes. |
| Long Abstract: Click Here |
| Poster W068 |
| IPASS: Error Tolerant NMR Backbone Resonance Assignment by Linear Programming |
| Xin Gao- University of Waterloo |
| Babak Alipanahi (University of Waterloo, David R. Cheriton School of Computer Science); |
| Short Abstract: This paper proposed a novel Integer Linear Programming (ILP) based NMR backbone resonance assignment method, IPASS, which guarantees to find the global optimalsolution under our problem setup. IPASS significantly outperforms the state-of-the-art assignment methods on both synthetic peak lists and real peak lists generated by automatic peak picking method. |
| Long Abstract: Click Here |
| Poster W070 |
| Improving Human Disease Gene Ranking by Cross-Species Function Prediction |
| Samira Jaeger- Humboldt-Universitaet zu Berlin |
| Stefan Kröger (Deutsches Rheuma-Forschungszentrum Berlin, Signal Transduction); Ulf Leser (Humboldt-Universitaet zu Berlin, Department of Computer Science); |
| Short Abstract: We propose a framework for disease gene ranking based on human interaction data and protein function to prioritize genes. The integration of predicted functions for uncharacterized proteins improves our ranking. We identify highly-ranked disease-related proteins that are weakly or not annotated and therefore cannot be captured by other methods. |
| Long Abstract: Click Here |
| Poster W071 |
| From the detection of functional regions towards function annotation in proteins |
| Guy Nimrod- Department of Biochemistry |
| Nir Ben-Tal (Tel Aviv University, Department of Biochemistry); Maya Schushan (Tel Aviv University, Department of Biochemistry); Christina Leslie (Memorial Sloan-Kettering Cancer Center, Computational Biology Program); András Szilágyi (Hungarian Academy of Sciences, Institute of Enzymology); |
| Short Abstract: We present a new method, and a web-server, for the identification of DNA binding proteins from 3D-structure. The method is based on various characteristics of the protein and the functional region predicted by the PatchFinder algorithm. We used it to predict DNA-binding proteins in the N-Func database of 'hypothetical proteins'. |
| Long Abstract: Click Here |
| Poster W072 |
| HOMOLOGY MODELLING AND MOLECULAR DYNAMIC SIMULATION TO MONILIOPHTHORA PERNICIOSA BETA-1,3-GLUCAN SYNTHASE |
| Catiane Souza- State University of Feira de Santana |
| Braz Hora-junior (State University of Santa Cruz, Biological Science); Bruno Andrade (State University of Feira de Santana., Biological Science); Maiza Lopes (State University of Santa Cruz, Biological Science); Cristiano Dias (State University of Santa Cruz, Biological Science); Carlos Pirovani (State University of Santa Cruz, Biological Science); Julio Cascardo (State University of Santa Cruz, Biological Science); Arist�teles G�es-Neto (State University of Feira de Santana, Biological Science); Alex Taranto (State University of Feira de Santana, Biological Science); |
| Short Abstract: The fungal cell wall, a complex structure composed by polysaccharides such as glucan synthase and chitin. The glucan synthase is targets to search for inhibitors in fungal pathogens. A model was constructed and refined. Its quality was evaluated by PROCHECK. The Ramachandran plot showed that the model was acceptible. |
| Long Abstract: Click Here |
| Poster W073 |
| Uncovering the Structure and Function of the Core Transcriptional Network That Maintains Pluripotency in Embryonic Stem Cells |
| Jaden Hastings- University of Oxford |
| No additional authors |
| Short Abstract: Pluripotency is known to be regulated by a particular set of transcription factors, including Nanog, Sox2 and Oct4 (POU5F1). Using both comparative modelling as well as ab initio molecular modelling methods, we generated the 3D structures of their human orthologs then applied docking methods to predict their interactions. |
| Long Abstract: Click Here |
| Poster W074 |
| Estimating the genome-wide preference of interaction between disordered proteins in a human protein-protein interaction network |
| Kana Shimizu- National Institute of Advanced Industrial Science and Technology (AIST) |
| Kazuhiko Fukui (National Institute of Advanced Industrial Science and Technology (AIST), Computational Biology Research Center (CBRC)); Hiroyuki Toh (Kyushu University, Medical Institute of Bioregulation); |
| Short Abstract: Intrinsic disorder is considered to play an important role in protein-protein interactions (PPIs). Although rigid structures have been expected to become identifiers for recognition on binding, this study revealed that the occurrence of interactions between disordered proteins is significantly frequent, by comparing an existing human PPI network with randomized networks. |
| Long Abstract: Click Here |
| Poster W075 |
| Bioinformatic Analysis of Sigma C Protein of Avian Reovirus Israeli Isolates Towards Novel Vaccine Production |
| Adva Yeheskel- Bioinformatics unit, The Faculty of Life Science, Tel Aviv University |
| Metsada Pasmanik-Chor (The Faculty of Life Science, Tel-Aviv University, Bioinformatics Unit); Dana Goldenberg (MIGAL-Galilee Technology Center, Department of Virology and Immunology); Jacob Pitcovski (MIGAL-Galilee Technology Center, of Virology and Immunology); |
| Short Abstract: Chicken reoviruses cause severe losses in avian industry. The present vaccines are inefficient. Sigma C protein from 28 Israeli viral isolates were sequenced. The aim of this study is to apply bioinformatic tools in order to better predict novel epitopes that would serve as better vaccination options. |
| Long Abstract: Click Here |
| Poster W076 |
| Prediction of super-secondary structure in α-helical and β-barrel transmembrane proteins |
| Van Du Tran- Laboratoire d'Informatique de l'Ecole Polytechnique |
| Jean-Marc Steyaert (Laboratoire d'Informatique de l'Ecole Polytechnique, Computer Science); Philippe Chassignet (Laboratoire d'Informatique de l'Ecole Polytechnique, Computer Science); |
| Short Abstract: We modeled the protein folding problem into finding the longest closed path in a graph with respect to some given permutation to predict the super-secondary structure in alpha-helical and beta-barrel proteins which may contain Greek key motifs. The algorithm is implemented and tested for the class of beta-barrel transmembrane proteins. |
| Long Abstract: Click Here |
| Poster W077 |
| Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods |
| Stefano Lise- University College London |
| Cedric Archambeau (University College London, Department of Computer Science); Massimiliano Pontil (University College London, Department of Computer Science); David Jones (University College London, Department of Computer Science); |
| Short Abstract: Protein-protein interactions are critically dependent on just a fewresidues (hot spots), which if mutated can disrupt complex formation.We present a novel computational approach to identify hot spot residues,given the structure of a complex. The approach combines the strengths ofmachine learning and energy-based methods. |
| Long Abstract: Click Here |
| Poster W078 |
| A novel index to evaluate the appropriateness of a set of homologous sequences for functional region prediction |
| Wataru Nemoto- Advanced Industrial Science and Technology |
| Wataru Nemoto (Advanced Industrial Science and Technology, Computational Biology Research Center); Hiroyuki Toh (Kyushu University, Medical Institute for Bioregulation); |
| Short Abstract: We developed a novel method to predict functional regions of a protein by using sequence and structure. Advantage of this method is that we can collect sequences for multiple sequence alignment automatically and objectively. We will discuss the benefits and the pitfalls of our method. |
| Long Abstract: Click Here |
| Poster W079 |
| Protein Sequence and Structure Optimisation in One Probabilistic Framework |
| Gundolf Schenk- University of Hamburg |
| Andrew Torda (University of Hamburg, ZBH - Centre for Bioinformatics); |
| Short Abstract: Protein structure prediction and sequence optimisation are two challenges which routinely appear to scare PhD students. We have used a fragment-based approach which turns both into a classic self-consistent field problem within a framework of descriptive statistics. |
| Long Abstract: Click Here |
| Poster W080 |
| Analysis of functional divergency in the EFG I and EFG II |
| Tõnu Margus- Tartu University |
| Maido Remm (Tartu University, Bioinformatics); Tanel Tenson (Institute of Technology at Tartu University, Antibiotics); |
| Short Abstract: EFG duplications in bacteria form four subfamilies: EFG-I, EFG-II, spdEFG1 and spdEFG2. We have first characterized an EFG subfamily (the EFG-II) which differs from the EFG-I (canonical EFG) by its high divergency in primary sequence. We highlight five differentially conserved positions which are related with altered functionality of the EFG-II |
| Long Abstract: Click Here |
| Poster W081 |
| PAUL: Protein structural alignment using integer linear programming and Lagrangian relaxation |
| Inken Wohlers- Centrum Wiskunde & Informatica |
| Lars Petzold (Freie Universität Berlin, Mathematics in Life Sciences Group); Francisco Domingues (Max-Planck-Institut für Informatik, Computational Biology and Applied Algorithmics Group); Gunnar Klau (Centrum Wiskunde & Informatica, Life Sciences Group); |
| Short Abstract: We present PAUL, a method for protein structural alignment that is based on aligning sparse protein distance matrices using integer linear programming and Lagrangian relaxation. PAUL is a novel, non-heuristic and mathematically sound approach that is competitive to or even outperforms other state-of-the-art structural alignment algorithms. |
| Long Abstract: Click Here |
| Poster W082 |
| Simulation of induced structural transitions in an isolated Kv1.2/2.1 voltage-sensor important for the gating mechanism |
| Christine Schwaiger- Center for Biomembrane Research |
| Pär Bjelkmar (Center for Biomembrane Research, Department of Biophysics and Biochemistry); Erik Lindahl (Center for Biomembrane Research, Department of Biophysics and Biochemistry); |
| Short Abstract: The Kv1.2/2.1 voltage-sensor movement is studied through an AFM-like technique. The voltage-sensor is pulled in two conformations (alpha/310), over the hydrophobic core proposed to be the gating free energy barrier, and the work distribution difference is compared. Additionally, residues responsible for the barrier are determined by utilizing core region mutations. |
| Long Abstract: Click Here |
| Poster W083 |
| Predicting helix-helix interactions from residue contacts in membrane proteins |
| Allan Lo- Academia Sinica |
| Yi-Yuan Chiu (Academia Sinica, Bioinformatics Lab., Institute of Information Science); Einar Andreas Rødland4 (University of Oslo, Centre for Cancer Biomedicine); Ping-Chiang Lyu (National Tsing Hua University, Institute of Bioinformatics and Structural Biology, Department of Life Sciences); Ting-Yi Sung (Academia Sinica, Bioinformatics Lab., Institute of Information Science); Wen-Lian Hsu (Academia Sinica, Bioinformatics Lab., Institute of Information Science); |
| Short Abstract: We present a novel two-level framework to predict residue contacts and helix-helix interactions in membrane proteins. Compared to the conventional direct method, this approach reduces both false positives and computational cost. This method can be used to guide helix-packing simulations and facilitate protein design for interaction with target transmembrane helices. |
| Long Abstract: Click Here |
| Poster W084 |
| Active Site Classification |
| Marc Roettig- Eberhard-Karls-University Tuebingen |
| Oliver Kohlbacher (Eberhard-Karls-University Tuebingen, Center for Bioinformatics); |
| Short Abstract: Active Site Classification (ASC) is a method to predict the specificity within an enzyme family usingsequence and structural information about the active site. We applied ASC to two enzyme families and could achieve improvements in classification accuracy and also interpretability of the models. |
| Long Abstract: Click Here |
| Poster W085 |
| Identification and comprehensive classification of Saccharomyces cerevisiae methyltransferome |
| Tomasz Wlodarski- University of Warsaw |
| Krzysztof Ginalski (University of Warsaw, Interdisciplinary Center for Mathematical and Computational Modelling); |
| Short Abstract: We have conducted comprehensive bioinformatics survey of all known and putative methyltransferases in S. cerevisiae genome and classified them into functional and structural classes. We identify several new methyltransferases and novel domains contexts and provide complete picture of methylation in S. cerevisiae. |
| Long Abstract: Click Here |
| Poster W086 |
| beta-strand segments prediction based on protein sequence and predicted neighboring structural information |
| Kanaka Durga Kedarisetti- University of Alberta |
| Marcin Mizianty (University of alberta, Electrical and Computer Engineering); Scott Dick (University of alberta, Electrical and Computer Engineering); Lukasz Kurgan (University of alberta, Electrical and Computer Engineering); |
| Short Abstract: Accurate prediction of beta-strands is an important step towards prediction of beta-sheets. We developed a novel sequence-based beta-strand predictor that exploits an ensemble of predicted local/global structural information. Our method improves SOVe and misses fewer strand segments when compared with current secondary structure predictors on two test sets including CASP8. |
| Long Abstract: Click Here |
| Poster W087 |
| Splitting statistical potentials to improve scoring of docking conformations |
| Elisenda Feliu Trijueque- Universitat de Barcelona |
| Baldomero Oliva (Pompeu Fabra University, Ciències experimentals i de la salut); Patrick Aloy (Institute for Research in Biomedicine, Structural and computational biology); |
| Short Abstract: We propose a new scoring function for rigid-body docking derived by splitting the usual residue-pair statistical potential as a sum of energy terms build upon local properties of the interacting aminoacids (exposure, secondary structure and hydrophobicity). The resulting scores are then combined into a final score. |
| Long Abstract: Click Here |
| Poster W088 |
| ModLink+: improving fold recognition by using protein-protein interactions |
| Oriol Fornes- GRIB-IMIM/UPF |
| Ramon Aragues (GRIB-IMIM/UPF, Structural Bioinformatics Lab); Jordi Espadaler (GRIB-IMIM/UPF, Structural Bioinformatics Lab); Marc A. Marti-Renom (GRIB-IMIM/UPF, Structural Bioinformatics Lab); Andrej Sali (UCSF, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences); |
| Short Abstract: The fold of a protein sequence can be predicted using different strategies. Here, we show how protein-protein interaction information can improve the fold recognition capacity of state-of-the-art methodologies. In addition, we show that our method can be applied large-scale (e.g. in yeast). |
| Long Abstract: Click Here |
| Poster W089 |
| Computational Identification of Local and Global RNA Motifs |
| Steffen Heyne- University of Freiburg |
| Rolf Backofen (University of Freiburg, Computer Science); Sebastian Will (University of Freiburg, Computer Science); |
| Short Abstract: Non-protein coding regions of bacteria as well as eukaryotes often contain important functional RNA elements. Both sequence and structure properties are important features of such RNAs. We present a new approach for the identification and motif-based comparison of such RNA elements. |
| Long Abstract: Click Here |
| Poster W090 |
| Predicting docking interactions between a plant defence protein and its ligands |
| Judit Kumuthini- CPGR |
| Melané Vivier (Stellenbosch University, IWBT); Abre de Beer (Stellenbosch University, IWBT); Albert Joubert (Stellenbosch University, IWBT); Reinhard Hiller (CPGR, CPGR); |
| Short Abstract: Protein-Protein interactions are useful in identifying the mechanism(s) involved in plant defence. This approach was to predict the interactions between a plant defence-protein and a plant pathogen. The binding-conformations of interaction complex of Endopolygalacturonases from B. cinerea and the polygalacturonase-inhibiting protein from grapevine were predicted using the crystalline-structure of the bean-PGIP as a model. |
| Long Abstract: Click Here |
| Poster W091 |
| New insights into coiled coil formation by means of support vector machines |
| Ingrid Abfalter- Johannes Kepler University Linz |
| Carsten Mahrenholz (Charite Berlin, Insititute for Medical Immunology); Ulrich Bodenhofer (Johannes Kepler University, Institute of Bioinformatics); Sepp Hochreiter (Johannes Kepler University, Institute of Bioinformatics); |
| Short Abstract: We use support vector machines and statistical methods to extract important amino acid sequence patterns that determine the olgimerization state of coiled coil proteins. These patterns are an important prerequisite for the rational design of drugs targeting coiled coil membrane fusion proteins from viruses like HIV and Avian Influenza. |
| Long Abstract: Click Here |
| Poster W092 |
| Identifying Functional Sites Common to the GCN5 Related N-Acetyltransferases (GNAT Super Family) Through Computational Methods |
| Domonique Bulls- North Carolina Agricultural & Technical State University |
| No additional authors |
| Short Abstract: This research focuses on the complexity of proteins and their active/functional sites. The GCN5-Related N-Acetyltransferases (GNAT Family) is a super family of proteins. The main goal is to identify functional sites and other structural motifs with assistance of computational methods. |
| Long Abstract: Click Here |
| Poster W093 |
| 3D Modeling of ribosomal RNA based on cryo-EM maps |
| Alexander Jarasch- Ludwig-Maximilians-Universität München |
| Roland Beckmann (Ludwig-Maximilians-Universität München, Gene Center); Fabrice Jossinet (Université Strasbourg, Institut de biologie moleculaire et cellulaire du CNRS); Elisabeth Villa (Max-Planck Institute for Biochemistry, Molecular Structural Biology); |
| Short Abstract: Modelling of RNA tertiary structure is still a difficult task. Here we present a workflow for RNA homology and de novo modelling followed by flexible fitting of the generated models into high-resolution cryo-EM maps using Molecular Dynamics Flexible Fitting (MDFF). |
| Long Abstract: Click Here |
| Poster W094 |
| Counting RNA pseudoknotted structures |
| Cédric Saule- Université Paris-Sud 11 and CNRS |
| Alain Denise (Université Paris-Sud 11 and CNRS, LRI & IGM); |
| Short Abstract: In 2004, Condon and coauthors classified RNA structure prediction algorithms allowing pseudoknots, according to the generality of the structure classes that they handle. We give formulas for the cardinality of several of these classes. This allows to better evaluate the tradeoff between computational complexity and expressive power of the algorithms. |
| Long Abstract: Click Here |
| Poster W095 |
| PhyloFacts: New Methods and Webservers |
| Ruchira Datta- UC Berkeley |
| Kimmen Sjölander (UC Berkeley, QB3 Institute); |
| Short Abstract: We present two new algorithms hosted within the PhyloFacts Phylogenomic Encyclopedias: http://phylofacts.berkeley.edu. INTREPID is a webserver for predicting functional sites which we have shown to produce higher accuracy on benchmark datasets. PHOG is a webserver for phylogenetic identification of orthologs that can be tuned to specific taxonomic distances. |
| Long Abstract: Click Here |
| Poster W096 |
| Combining Kernels for SVM-based Classification of protein structral sequences |
| Quan Le- University College Dublin |
| Patrice Koehl (University of California, Davis, Department of Computer Science and Genome Center); Gianluca Pollastri (University College Dublin, School of Computer Science and Informatics); |
| Short Abstract: An appealing approach to classify protein structures is to map each structure to a sequence of letters representing structural motifs, thenclassify these sequences using sequence based classifiers. Adopting an informative sequence representation, we show that the SVM with a kerned combined from different spectrum kernels significantly outperforms a SVM using spectrum kernel. |
| Long Abstract: Click Here |
| Poster W098 |
| Protein secondary structure prediction evaluation using a new tool - SSPE |
| Bogumil Konopka- Wroclaw University of Technology |
| Witold Dyrka (Wroclaw University of Technology, Faculty of Fundamental Problems of Technology); Jean-Christophe Nebel (Kingston University London, Faculty of Computing, Information Systems and Mathematics); Malgorzata Kotulska (Wroclaw University of Technology, The Faculty of Fundamental Problems of Technology); |
| Short Abstract: Secondary structure prediction is a significant stage in protein three-dimensional structure prediction. We have developed software for evaluating the efficiency of secondary structure predictors using segment overlap and standard per residue evaluation parameters. A standard evaluation procedure was proposed to validate prediction of four secondary structure predictors. |
| Long Abstract: Click Here |
| Poster W099 |
| An efficient on-line software for automatic prediction of non-coding RNA secondary structures |
| Fariza Tahi- CNRS/University of Evry/Genopole |
| No additional authors |
| Short Abstract: We propose an efficient algorithm and system called Tfold (http://tfold.ibisc.univ-evry.fr/TFold), for predicting non-coding RNA secondary structures. Tfold combines conservation, covariation and thermodynamic criteria for searching for stems including all kinds of pseudo-knots. Tfold is very competitive in terms of results quality and of time complexity comparing to existing software. |
| Long Abstract: Click Here |
| Poster W100 |
| Transmembrane protein structure determination guided by sparse experimental restrains. |
| Dominik Gront- University of Warsaw |
| David Baker (University of Washington, Department of Biochemistry); |
| Short Abstract: We combined Rosetta protein structure prediction methodology with chemical shifts measured by solid-state NMR experiments to build structures of transmembrane proteins. We used anisotropic chemical shifts and couplings to guide model building. Our primary results show the great potential in anisotropic NMR data; the structure of test proteins can be calculated at the great level of accuracy. |
| Long Abstract: Click Here |
| Poster W101 |
| Structural insight into the binding mode between the targeting domain of ALE-1 (92AA) and pentaglycine of peptidoglycan |
| Hideki Hirakawa- Kazusa DNA Research Institute |
| Hidenori Akita (Kyushu University, Graduate School of Genetic Resource Technology); Tamaki Fujiwara (Hiroshima University, Department of Bacteriology); Motoyuki Sugai (Hiroshima University, Department of Bacteriology); Satoru Kuhara (Kyushu University, Graduate School of Genetic Resource Technology); |
| Short Abstract: ALE-1 is a glycylglycine endopeptidase that selectively lyses the pentaglycine of peptidoglycan of Staphylococcus aureus, which is expected to be a next generation antibacterial agent.We proposed a mode of binding between 92AA (binding domain of ALE-1) and the pentaglycine of peptidoglycan by a binding simulation. |
| Long Abstract: Click Here |
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