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ISMB 2005 Posters

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ISMB 2005 Posters 1 RNA and Protein Structural Biology Poster A-2 (There will also be an oral presentation of this poster.) A Conserved Sparse Dicodon Framework Which Correlates Sequence and Structure: Implications for Gene Finding David Halitsky (Cumulative Inquiry, Inc); Arthur Lesk (Dept of Haemaology, CIMR); Jacques Fresco (Princeton University) Abstract: Analysis of di-codon pairs in mRNA sequences can identify structurally similar features in the encoded proteins via a sparse signal characterized by number and order of certain dicodons occuring within codon subsequences of specific lengths. The signal reliably detects structurally similar features with virtually no underlying sequence similarity. Poster A-3 De Novo Assembly of Transmembrane Helices of Polytopic Membrane Proteins Using Sequence Conservation Patterns Yungki Park (Center for Bioinformatics, Saarland University); Volkhard Helms (Center for Bioinformatics, Saarland University) Abstract: A novel two-step method for modeling structures of transmembrane helix bundle proteins was developed: generation of libraries of folds and specification of the best fold based on sequence conservation patterns. For a broad spectrum of test proteins, it consistently generated model structures within CA RMSDs of 3 5 . Poster A-4 Protein-Protein Docking Methods Used to Study Complex Protein Interactions Dana Haley-Vicente (Accelrys); Tim Glennon (Accelrys) Abstract: Understanding the protein-protein interactions is important for insights into signal transduction pathways. Here we have applied protein-protein docking, Evolutionary trace, fold, hydrophobic, and electrostatics analysis to determine and understand the interaction between a regulator of G-protein signaling protein and the alpha subunit of G-proteins. Poster A-5 Comprehensive LAboratory information Management system (CLAM): the Structural Module Tjaart de Beer (University of Pretoria); Fourie Joubert (University of Pretoria) Abstract: The aim of this project is to construct an Open Source, web based functional genomic information system called CLAM (Comprehensive LAboratory information Management). CLAM will contain modules for genotyping, proteomics, genetics, phylogenetics, microarray, comparative genomics and structural biology data analysis. This poster will focus on the structural module in CLAM. Poster A-6 Metal binding sites: pre-organized scaffolds in the unbound state Mariana Babor (Weizmann Institute of Science); Harry Greenblatt (Weizmann Institute of Science); 1 Marvin Edelman (Weizmann Institute of Science); Vladimir Sobolev (Weizmann Institute of Science) Abstract: Protein metal binding sites in the unbound state, and their rearrangements upon metal binding were analyzed. More than 40% of the metal binding sites show a capacity for flexibility, but in the vast majority of cases, part of the first coordination shell is already in place in the pre-bound form. Poster A-7 Functional Prediction of Protein Mutants Using a Four-Body Potential Majid Masso (George Mason University); Iosif Vaisman (George Mason University) Abstract: Studies exploring single point mutants of HIV-1 protease and T4 lysozyme suggest that prediction of mutant enzyme catalytic activity is realizable by employing supervised learning in conjunction with mutant attribute vectors, based on a four-body statistical potential, that characterize constituent amino acid environmental changes from wild-type. Poster A-8 (There will also be an oral presentation of this poster.) Enzyme Mechanism Annotation and Classification Daniel Almonacid (Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge); Gemma Holliday (Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge); Peter Murray-Rust (Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge); Janet Thornton (EMBL-EBI, Wellcome Genome Campus); John Mitchell (Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge) Abstract: MACiE is a unique database containing enzyme-catalysed reaction mechanisms. Reaction steps as well as overall reactions are included. Data mining of this database has already provided a better insight into the nature’s catalytic diversity. Our ongoing work addresses the evolution and classification of enzymes. Poster A-9 Automated creation of in silico analogue ligand libraries from a lead molecule template Wolf Cochrane (University Pretoria); Fourie Joubert (University Pretoria) Abstract: LIGLIB (LIGand LIbrary Builder) is an open source tool that allows users to create an in silico library of molecules that are analogues of a lead chemical compound given as input to the software. The software is available as a plug-in to chimera. Poster A-11 (There will also be an oral presentation of this poster.) A novel approach to structural alignment using realistic structural and environmental information Yu Chen (Bioinformatics program, University of Michigan); Gordon Crippen (College of Pharmacy, University of Michigan) Abstract: We find a new structural alignment approach using realistic structural as well as environmental information. Statistics are defined to measure the goodness of alignments in structure cores. With this method, we can distinguish structures in different oligomeric states, and can flexibly align multiple domain proteins without domain splitting. Poster A-12 Identifying Functional Signatures from Structural Alignments Kai Wang (University of Washington); Ram Samudrala (University of Washington) Abstract: We developed a method called Functional Signature from Structural Alignments (FSSA), to estimate the log odds of a residue being functionally important versus structurally important. The FSSA signatures can be used to interpret the functional importance of each residue, or classify proteins into functional categories. 2 Poster A-13 Doing a double take: function based target selection for structural genomics Iddo Friedberg (The Burnham Institute); Phillip Lord (University of Manchester); Andrei Osterman (The Burnham Institute); Adam Godzik (The Burnham Institute) Abstract: Structural genomics target selection schemes usually favor proteins predicted to have new folds. Here we argue that more targets should be selected within a given fold, to provide accurate templates not only for fold space, but also for function space, which is more finely grained. Poster A-14 A new set of docking potentials for efficient discrimination between native and non-native conformations of protein complexes Dror Tobi (Department of Computational Biology School of Medicine, University of Pittsburgh); Ivet Bahar (Department of Computational Biology School of Medicine, University of Pittsburgh) Abstract: We generated putative docked complexes for a set of 63 non-reduncdant complexes, which were used in a linear programming algorithm to generate coarse-grained Docking Potentials. The resulting set of potentials show promising results for discriminating the native complex among decoys generated with the unbound form of the interacting proteins. Poster A-16 Structural identification and prediction of amphipathic alpha-helices Mamta Bajaj (School of Biological Sciences, University of Nebraska-Lincoln); Hideaki Moriyama (Department of Chemistry, University of Nebraska-Lincoln); Etsuko Moriyama (School of Biological Sciences and Plant Science Initiative, University of Nebraska-Lincoln) Abstract: We developed a new method for identifying amphipathic alpha-helices based on PDB coordinate information, and identified 26 amphipathic alpha-helices that are not annotated as amphipathic alpha-helices in the PDB. Based on this dataset, we developed a new prediction method for amphipathic alpha-helices from primary structure information. Poster A-17 Accurate Recognition of Protein-DNA Interaction Using Optimized Potential with Multi-body Consideration Zhijie Liu (Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia); Ying Xu (Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia) Abstract: A knowledge-based potential that considers the distance-dependent multi-body interactions was developed to quantitatively evaluate the binding affinity between protein and DNA. The potential achieved significant agreement between predictions and the experimental data, and succeeded in identification of DNA binding motifs of transcription factors in the genome-scale. Poster A-18 Few strict rules determine permissible arrangements of strands in the Sandwich Proteins Yih-Shien Chiang (Department of Health Informatics, SHRP, University of Medicine and Dentistry of New Jersey); Tatyana Gelfand (Department of Mathematics, Rutgers University); Thanasis Fokas (Department of Applied Mathematics and Theoretical Physics, University of Cambridge); Alexander Kister (Department of Health Informatics, SHRP, University of Medicine and Dentistry of New Jersey); Israel Gelfand (Department of Mathematics, Rutgers University) Abstract: Analysis of the arrangements of strands in beta-sandwich proteins has led to propose a set of rules, which determine the main principles of the packing of strands in structures. These constraint rules allow one to determine all permissible motifs of the sandwich-like proteins. Keywords : Protein prediction, supersecondary structure. 3 Poster A-19 A Protein Structure Comparison system using 3D LRA Chan-Yong Park (Electronics and
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