19th Annual International Conference on
Intelligent Systems for Molecular Biology and
10th European Conference on Computational Biology

Accepted Posters

Category 'V'- Structural Genomics'
Poster V1
P.R.E.S.S.--- An R-package for Exploring Residual-Level Protein Structural Statistics

yuanyuan huang Iowa State University
Yuanyuan huang (Iowa State University)
Short Abstract: P.R.E.S.S. is an R package developed to allow researchers to get access to and manipulate on a large set of statistical data on protein residue-level structural properties such as residue-level virtual bond lengths, virtual bond angles, and virtual torsion angles. A large set of high-resolution protein structures are downloaded and surveyed. Their residue-level structural properties are calculated and documented. The statistical distributions and correlations of these properties can be queried and displayed. Tools are also provided for modeling and analyzing a given structure in terms of its residue-level structural properties. In particular, new tools for computing residue-level statistical potentials and displaying residue-level Ramachandran-like plots are developed for structural analysis and refinement. P.R.E.S.S. will be released in R as an open source software package, with a user-friendly GUI interface, accessible and executable by a public user in any R environment. Further development on a website of database interface is also included.
Poster V2
DIBER: protein, dna or both?

Grzegorz Chojnowski International Institute of Molecular and Cell Biology in Warsaw
Matthias Bochtler (Cardiff University, Schools of Chemistry and Biosciences);
Short Abstract: Protein crystallographers who work on protein-DNA complexes routinely face the problem that co-crystallization of protein and DNA does not necessarily guarantee that both components will be incorporated into any macromolecular crystals that can be grown. We present a computer program and a web server DIBER which provides a way to judge DNA content based on a diffraction data before phase information becomes available. Our method uses a support vector machine classifier trained on a very large set of data from PDB to make the best possible prediction with minimal input form the user.

Long Abstract: Click Here

Poster V3
Identification of functional subclasses in the ribulose-phosphate binding barrel (RPBB) superfamily

Joslynn Lee Northeastern University
Short Abstract: The ability to predict the function of a protein from its 3D structure is an important problem in the post-genomic era. This paper describes a computational method for the identification of function for proteins within a superfamily. Superfamilies are defined as a group of evolutionarily related proteins with similar 3D structures. Although the proteins within a given superfamily all have similar structures, there can be enormous functional diversity within a superfamily. The ribulose-phosphate binding barrel (RPBB) superfamily consists of eight subclasses; each of the eight subclasses represents a different type of biochemical function. The subclasses are structurally similar but can be distinguished using our approach. The computational approach to understanding the functional diversity in this superfamily is based on a local structural analysis at the interaction sites of the individual proteins. First, Theoretical Microscopic Titration Curves (THEMATICS) and Information-theoretic Tree Traversal for Protein Functional Site Identification (INTREPID) are combined with Partial Order Optimum Likelihood (POOL) to predict the residues involved in catalysis and/or ligand binding for each protein structure in the superfamily. Then, the 3D structures of the proteins are aligned. The predicted active residues are labeled on the alignment. From this labeled alignment, patterns emerge that enable the RPBB superfamily to be sorted into functional subclasses. Applications to Structural Genomics (SG) proteins of unknown or uncertain function are reported. The SG protein annotations are determined to be correct or incorrect using our chemical similarity scoring function on the residues in the spatial region of the predicted functional site.
Poster V4
Exhaustive Structural Comparison of DNA-binding Sites in Proteins

Ryoichi Minai Shizuoka University
Tokumasa Horiike (Shizuoka University, GRL);
Short Abstract: We developed a method for the structural alignment of atoms in the solvent-accessible surface of proteins, and carried out exhaustive structural comparison for DNA-binding sites of structure-known proteins for revealing the DNA-recognition mechanism.

Firstly, the three-dimensional coordinate data of 1805 DNA/protein complexes were obtained from the protein data bank.

After that 7361 DNA-binding sites were identified from these complexes and 1066 sites of them were selected for the nonredundant dataset. For each pair of the nonredundant DNA-binding site, the structural similarity scores were calculated by using our alignment method.

Furthermore, hierarchical clustering analysis with these similarity scores was carried out. As a result, 28 clusters were obtained. Some clusters indicated the relationships between structures and functions because the same functional proteins concentrated in these clusters.
We focused on the clusters that contain the DNA endonuclease, the DNA-binding transcription factor, and the histone-like protein and searched for their shared structure.
Poster V5
The Protein Model Portal and CAMEO - Continuous Automated Evaluation of Modeling and Quality Estimation Servers

Lorenza Bordoli SIB Swiss Institute of Bioinformatics
Torsten Schwede (SIB Swiss Institute of Bioinformatics) Lorenza Bordoli (SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel); Jürgen Haas (SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel); Khaled Mostaguir (SIB Swiss Institute of Bioinformatics, Biozentrum University Basel); Konstantin Arnold (SIB Swiss Institute of Bioinformatics, Biozentrum University Basel); Pascal Benkert (SIB Swiss Institute of Bioinformatics, Biozentrum University Basel);
Short Abstract: The Protein Model Portal (PMP; http://www.proteinmodelportal.org) has been developed as a component of the Nature PSI structural Biology knowledgebase to foster effective use of protein structure models in biomedical research by providing convenient and comprehensive access to structural information. For a protein of interest, both experimental structures from the PDB and theoretical models can be searched simultaneously, and analyzed for structural variation. The current release allows searching 71’800 experimental structures and 15.4 million models provided by 10 different modeling resources for 3.8 million distinct UniProt entries.
Here, we present several new developments in Protein Model Portal supporting interactive modeling, model quality estimation, and model quality assessment. Ultimately, the accuracy of a structural model determines its usefulness for specific applications in biomedical research. PMP interfaces to several established model quality estimation tools to apply consistent assessment and validation criteria to the structural models available for a specific protein. PMP further provides a service for continuous evaluation of the modeling and model quality estimation tools (CAMEO; Continuous Automated Model EvaluatiOn). The continuous retrospective analysis of the accuracy and reliability of services for protein modeling and quality estimation helps the developers of these methods to improve their approaches, and the users to select the most appropriate tools for their applications.
Poster V6
The Biochemical Algorithms Library (BALL) - Rapid Application Development in Structural Bioinformatics

Andreas Hildebrandt Johannes-Gutenberg Universität Mainz
Anna Katharina Dehof (Saarland University, Center for Bioinformatics); Daniel Stöckel (Saarland University, Center for Bioinformatics); Stefan Nickels (Saarland University, Center for Bioinformatics); Sabine Mueller (Saarland University, Center for Bioinformatics); Marcel Schumann (Eberhard-Karls University Tübingen, Applied Bioinformatics); Hans-Peter Lenhof (Saarland University, Center for Bioinformatics); Oliver Kohlbacher (Eberhard-Karls University Tübingen, Applied Bioinformatics);
Short Abstract: Developing programs for structural bioinformatics is a difficult and often tedious task. Even if the algorithms have been carefully designed, the programmer has to solve a variety of complex and recurring problems not fundamentally related to the algorithm at hand, but necessary for real-world applications.

With the Biochemical Algorithms Library (BALL), we present a versatile C++ class library for structural bioinformatics that is supplemented with a Python interface for scripting functionality and a number of applications like the molecular modeler BALLView.

In recent years, BALL has seen a significant increase in functionality and substantial useability improvements. It has been ported to further operating systems; indeed, it currently supports all major brands. Moreover, BALL has evolved from a commercial product into a free-of-charge, open source software licensed under the Lesser GNU Public License (LGPL).

The current version (1.4.1 at the time of writing) contains more than 730 classes and more than 700,000 lines of code. Of these, we want to briefly highlight some of BALL's most important features and will show some ways in which the use of such an rapid application development framework can simplify the life of scientists and developers.
Poster V7
SymD server: a platform for detecting internally symmetric protein structures

Chin-Hsien (Emily) Tai National Cancer Institute
Rohit Paul (National Cancer Institute, Office of Information Technology); Dukka K.C. (National Cancer Institute, Center for Cancer Research); Jeffery Shilling (National Cancer Institute, Office of Information Technology); Byungkook Lee (National Cancer Institute, Center for Cancer Research);
Short Abstract: Many protein chains are made of repeating units of similar structures arranged in a beautifully symmetric manner. The mechanism of such an arrangement, the biological function, and the evolutionary history of symmetric proteins are largely unknown. To answer these questions, we first developed a program, called SymD, to detect internally symmetric protein structures (Kim et al., BMC Bioinformatics, 2010). Here, we report on the development of the SymD web server (http://symd.nci.nih.gov), a dynamic platform based on Galaxy to determine if a protein is symmetric and to visualize the structure interactively. The input can be a user’s own structure, either experimentally determined or computationally modeled. Structures can also be fetched from PDB, SCOP or CATH protein structure database. A protein structure is aligned to itself after circularly permuting the second copy by all possible number of residues. SymD finds the transformation that will make the original and the permuted structures maximally aligned. Such transformation is generally a combination of a rotation around an axis and a translation along the axis. SymD then reports the rotation axis, the number of aligned residues between original and transformed structures, and other scores that measure the degree of the structural alignment. It also gives the rotation angle, the transformed structure in PDB format and the alignment in FASTA format. Users can view the structure in Jmol and the alignment in Jalview on line interactively. They are able to download the results for further analysis as well.

Accepted Posters

Attention Poster Authors: The ideal poster size should be max. 1.30 m (130 cm) high x 0.90 m (90 cm) wide. Fasteners (Velcro / double sided tape) will be provided at the site, please DO NOT bring tape, tacks or pins. View a diagram of the the poster board here

Posters Display Schedule:

Odd Numbered posters:
  • Set-up timeframe: Sunday, July 17, 7:30 a.m. - 10:00 a.m.
  • Author poster presentations: Monday, July 18, 12:40 p.m. - 2:30 p.m.
  • Removal timeframe: Monday, July 18, 2:30 p.m. - 3:30 p.m.*
Even Numbered posters:
  • Set-up timeframe: Monday, July 18, 3:30 p.m. - 4:30 p.m.
  • Author poster presentations: Tuesday, July 19, 12:40 p.m. - 2:30 p.m.
  • Removal timeframe: Tuesday, July 19, 2:30 p.m. - 4:00 p.m.*
* Posters that are not removed by the designated time may be taken down by the organizers and discarded. Please be sure to remove your poster within the stated timeframe.

Delegate Posters Viewing Schedule

Odd Numbered posters:
On display Sunday, July 17, 10:00 a.m. through Monday, June 18, 2:30 p.m.
Author presentations will take place Monday, July 18: 12:40 p.m.-2:30 p.m.

Even Numbered posters:
On display Monday, July 18, 4:30 p.m. through Tuesday, June 19, 2:30 p.m.
Author presentations will take place Tuesday, July 19: 12:40 p.m.-2:30 p.m

Want to print a poster in Vienna - try these options:

Repacopy- next to the congress venue link [MAP]

Also at Karlsplatz is in the Ring Center, Kärntner Str. 42, link [MAP]

If you need your poster on a thicker material, you may also use a plotter service next to Karlsplatz: http://schiessling.at/portfolio/

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