Accepted Posters

Category 'V'- Structural Genomics'

Poster V01

Dali server in 2009

Liisa Holm- University of Helsinki

Hitomi Hasegawa (University of Helsinki, Institute of Biotechnology);

Short Abstract: The Dali server is a network service for comparing protein structures in 3D. It has been used to systematically scan newstructures against the Protein Data Bank (PDB) for some 15 years. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences.

Long Abstract: Click Here

Poster V02

A Protein Surface Comparing Method using Structure Factor

KWANG SU JUNG- CBITRC, CHUNGBUK NATIONAL UNIV

NAM HEE YU (CBITRC, CHUNGBUK NATIONAL UNIV, COMPUTER SCIENCE); KEUN HO RYU (CBITRC, CHUNGBUK NATIONAL UNIV, COMPUTER SCIENCE); YONG JE CHUNG (CBITRC, CHUNGBUK NATIONAL UNIV, LIFE SCIENCE);

Short Abstract: Proteins need to combine other substrates or proteins to perform their function, and proteins which have similar actives sites have similar function.We suggest a method to compare partial surfaces of proteins using structure factors and phase angles. Our work can be adopted to produce proteins which have more functionality.

Long Abstract: Click Here

Poster V03

Public archive for structural variants.

Jonathan Hinton- European Bioinformatics Institute

Ilkka Lappalainen (EBI, EGA); Mario Caccamo (EBI, EGA); Lars Feuk (The Hospital for Sick Children, The Centre for Applied Genomics); Vasudev Kumanduri (EBI, EGA); Paul Flicek (EBI, Vertebrate Genomics); Margie Manker (The Hospital for Sick Children, The Centre for Applied Genomics); Steve Scherer (The Hospital for Sick Children, The Centre for Applied Genomics);

Short Abstract: In resent years we have seen an explosion in studies describing human structural variation. The increasing quality and quantity brings new insight to our understanding of the complexity of the human genome. We propose a permanent archive to store, accession and distribute the different types of experimentally identified structural variation.

Long Abstract: Click Here

Poster V04

A new software to study atom-atom interactions in protein complex interfaces

Tomas Norambuena- Pontificia Universidad Catolica de Chile

Francisco Melo (Pontificia Universidad Catolica de Chile, Molecular Genetics and Microbiology);

Short Abstract: We have developed a new computer software intended for the analysis and study of binding interfaces in different molecular complexes such as protein-nucleic acids and protein-small ligands. The software is highly customizable and has many features to further characterize the type of interactions that occur at the complex interface.

Long Abstract: Click Here

Poster V05

Toward the prediction of the survival of alternative splice variants of human proteins

Hedi Hegyi- Institute of Enzymology

Lajos Kalmar (Inst Enzymology, N/A);

Short Abstract: According to current estimations 95% of multi-exonic human genes undergo alternative splicing with 6 splice variants/protein. However, only 11 human isoform structures are in PDB. We analyze human splice variants for length and hydrophobic surface energies. We find several limiting constraints to apply to eliminate/confirm the survival of many isoforms.

Long Abstract: Click Here

Poster V06

STRUCTURE-BASED PREDICTION OF ANTIBODY EPITOPES

Petr Ponomarenko- Novosibirsk State University, Russia

Ruben Abagyan (The Scripps Research Institute, Molecular Biology); Philip Bourne (University of California, Skaggs School of Pharmacy & Pharmaceutical Science and Sun Diego Supercomputer Center); Julia Ponomarenko (University of California, Skaggs School of Pharmacy & Pharmaceutical Science and Sun Diego Supercomputer Center);

Short Abstract: We present a novel method for antibody epitope prediction in protein antigens of given structure. The method uses sequence and structural properties of epitopes known from 3D structures of antibody-protein complexes and supervised machine learning. The performance of the method exceeds other available structure-based methods for antibody epitope prediction.

Long Abstract: Click Here

Poster V07

Considerations for algorithm selection and experimental design in detection of copy number variations in cancer.

Beth Wilmot- Oregon Health & Science University

Ping-Hsun Hsieh (Oregon Health & Science University, Oregon Clinical and Translational Research Institute); Shannon McWeeney (Oregon Health & Science University, Oregon Clinical and Translational Research Institute, Div. of Biostatistics, Dept. of Public Health and Prev. Med);

Short Abstract: DNA copy number variations (CNVs) are a significant and ubiquitous source of human genetic variation in cancer. We used Affymetrix 6.0 SNP arrays to evaluate how the choice of algorithm and associated parameters impacted the analysis of acquired Uniparental Disomy (aUPD) in clinically phenotyped myeloproliferative disorder (MPD) patient samples.

Long Abstract: Click Here

Poster V08

Identify the dynamic domain of protein by the protein fixed-point model

Chih-Hao Lu- China Medical University

No additional authors

Short Abstract: We have developed a hybrid approach combined with structure and dynamics features for classification of protein domains. We use the protein fixed-point model and the clustering method to cluster the residues which belong to the same dynamic domain. Our approaches are quite simple and efficient for protein domain decomposed.

Long Abstract: Click Here

Poster V09

Identifying structural elements associated with RNA families sharing biological function

Miler Lee- University of Pennsylvania School of Medicine

Junhyong Kim (University of Pennsylvania, Biology);

Short Abstract: We explore the extent to which RNA structural motifs can be associated with biological function across different RNA families. Using a compact encoding, we decompose RNA structures into parts and show that particular motifs are enriched for functional attributes as defined by an ontology we automatically generate from Wikipedia.

Long Abstract: Click Here

Poster V10

Homology modelling based protein functional residues prediction

Raquel Minardi- Genoscope / IG / CEA

No additional authors

Short Abstract: We propose a methodology to predict protein function based on structural data. We build 3D homology-based models for the family, computing and analyzing structural cavities using HMM, aligning their structures and clustering the family into subgroups of similar cavity residues profiles. After that we use a molecular docking approach with possible ligands.

Long Abstract: Click Here

Accepted Posters

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