Brief info about the seminar SCHEDULE: 30 OCT: Finalize assignment of papers for each student. WEEK 1 DEC. 4: FUNCTIONAL PREDICTION: Naomi, FFF MISCELANEOUS: Alexei Krasnopolski no. 37. Strategies for the development of a peptide computer. WEEK 2 DEC. 11 STRUCTURE ALIGNMENTS AND CLASSIFICATIONS AMIR no. 30. Automated Discovery of Structural Signatures of Protein Fold and Function. Marcel Turcotte, Stephen H. Muggleton, Michael J. E. Sternberg , JMB 306, 3, 591. Sigalit Dadon: Seq. Alig, DP. WEEK 3 DEC. 18 SEQUENCE ALIGNMENTS, MULTIPLE ALIGNMNETS BLAST Vitali Shenzrov no. 36. Comparison of DNA, problems, Miller, Bioinf. 17,5,391. SOFI. Ofer Darzi no. 39. A new approach to seq. comparison , Arslan, 17, 4, 327. WEEK 4 DEC. 25 STRUCTURE ALIGNMENTS AND CLASSIFICATIONS Einat Reich no. 31. A Novel Method for Sampling Alpha-helical Protein Backbones Boris Fain, Michael Levitt , JMB, 305,2, 191. Zvi Kogan no. 10. Automated multiple structure alignment and detection of a common substructural motif. Nathaniel Leibowitz, Zipora Y. Fligelman, Ruth Nussinov, Haim J. Wolfson. Proteins 43, 2, 235. WEEK 5 JAN. 1 FOLD RECOGNITION, FOLDING Oren Uri no. 38. Multi-class, FR using vector machines, Ding, Bioinf. 17,4,349. Tomer Paz no. 41. Clustering Protein Sequence-Structure prediction by transitive homology. WEEK 6 JAN. 8 FOLD RECOGNITION, FOLDING Lior Malka no. 50 pcons, prot. sci. 10,2354, Lundstrom et al. GENOMIC ISSUES Vladimir Lipez. no. 33. GeneOrder, Mazumder, Bioinfo, 17, 2, 162. WEEK 7 Jan. 15. Hagit Krauz : GENETIC ALGORITHMS, SHEMATA, Prisoner Dylemma. Gral Theory + small examples. with Mike TO LECTURE BEFORE DEC. 25). Vaisman Amit 22. Surface Map Comparison: Studying Function Diversity of Homologous Proteins Krzysztof Pawowski, Adam Godzik . JMB, 309, 3, 793. OR TANDEM REPEATS WEEK 8 DOCKING , PROTEIN SURFACES Pini BenDavid no. 23. FLEX E: Efficient Molecular Docking Considering Protein Structure Variations Holger Clau_en, Christian Buning, Matthias Rarey, Thomas Lengauer , JMB, 308, 2, 377. Yehuda Itzhaki no. 35. Predicting Prot. interactions, Bock, Bioinf. 17, 5, 455. WEEK 9 DOCKING , PROTEIN SURFACES Mike Tebeka, no. 11. Protein docking using a genetic algorithm. Eleanor J. Gardiner, Peter Willett, Peter J. Artymiuk. Proteins 44,1, 44. with Hagit. Grinshpon Tal no. 15. Correlated Sequence-signatures as Markers of Protein-Protein Interaction . Einat Sprinzak, Hanah Margalit . JMB 311,4, 681. (NEED WEEK 10 PREDICTION Nadav Popelwel no. 32. Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes Anders Krogh, Bjvrn Larsson, Gunnar von Heijne, Erik L. L. Sonnhammer , JMB 305,3,587. LIST OF PAPERS AVAILABLE BY TOPICS: FOLD RECOGNITION, FOLDING 1. Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading. Yibing Shan, Guoli Wang, Huan-Xiang Zhou. Proteins, 42,1, 23-37. 6. Defrosting the frozen approximation: PROSPECTOR - A new approach to threading. Jeffrey Skolnick, Daisuke Kihara. Proteins 42, 3, 319-331. 8. Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Richard Bonneau, Charlie E.M. Strauss, David Baker. Proteins 43,1, 1. 12. Linear programming optimization and a double statistical filter for protein threading protocols. Jaroslaw Meller, Ron Elber. Proteins 45,2, 241. 21. FUGUE: Sequence-structure Homology Recognition Using Environment-specific. Substitution Tables and Structure-dependent Gap Penalties . JMB, 310,1,243. DOCKING , PROTEIN SURFACES 3. Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation. Andrew I. Su, David M. Lorber, G. Scott Weston, Walter A. Baase, Brian W. Matthews, Brian K. Shoichet. Proteins, 42, 2,279-293. 7. Prediction of protein surface accessibility with information theory. Hossein Naderi-Manesh, Mehdi Sadeghi, Shahriar Arab, Ali A. Moosavi Movahedi. Proteins, 42, 4, 452. 9. Residue frequencies and pairing preferences at protein-protein interfaces. Fabian Glaser, David M. Steinberg, Ilya A. Vakser, Nir Ben-Tal. Proteins 43,1,89. 25. Three-dimensional Cluster Analysis Identifies Interfaces and Functional Residue Clusters in Proteins Ralf Landgraf, Ioannis Xenarios, David Eisenberg , JMB< 307, 5, 1487. 29. ConSurf: An Algorithmic Tool for the Identification of Functional Regions in Proteins by Surface Mapping of Phylogenetic Information Aharon Armon, Dan Graur, Nir Ben-Tal , JMB, 307, 1, 447. --. Protein Surface Amino Acid Compositions Distinctively Differ Between Thermophilic and Mesophilic Bacteria Satoshi Fukuchi, Ken Nishikawa . JMB, 309,4, 835. STRUCTURE ALIGNMENTS AND CLASSIFICATIONS 4. Protein structural alignments and functional genomics. James A. Irving, James C. Whisstock, Arthur M. Lesk. Proteins, 42, 3, 378-382. 5. Protein structural domains: Analysis of the 3Dee domains database. Uwe Dengler, Asim S. Siddiqui, Geoffrey J. Barton. Proteins 42, 3, 332-344. 18. Defining Linear Segments in Protein Structure . William R. Taylor . JMB, 310, 5, 1135. --. Evolution of Function in Protein Superfamilies, from a Structural Perspective Annabel E. Todd, Christine A. Orengo, Janet M. Thornton , JMB, 307,4, 1113. 16. Automated Structure-based Prediction of Functional Sites in Proteins: Applications to Assessing the Validity of Inheriting Protein Function from Homology in Genome Annotation and to Protein Docking. Patrick Aloy, Enrique Querol, Francesc X. Aviles, Michael J. E. Sternberg . JMB, 311, 2, 395. 34. SCORE, Predicting cores Deane, Bioinfo, 17,6,541. PREDICTION 13. SNAPping up Functionally Related Genes Based on Context Information: A Colinearity-free Approach. G. Kolesov, H.-W. Mewes, D. Frishman . JMB 311, 4, 625. 17. Extending the Accuracy Limits of Prediction for Side-chain Conformations . Zhexin Xiang, Barry Honig . JMB< 311, 2, , 421. 24. A Novel Method of Protein Secondary Structure Prediction with High Segment Overlap Measure: Support Vector Machine Approach Sujun Hua, Zhirong Sun . JMB, 308, 2, 397. GENOMIC ISSUES 28. Prospects for ab initio Protein Structural Genomics Kim T. Simons, Charlie Strauss, David Baker , JMB, 306,5. 20. Domain Combinations in Archaeal, Eubacterial and Eukaryotic Proteomes . Gordana Apic, Julian Gough, Sarah A. Teichmann . JMB, 310, 2, 311. 19. Sructural and Functional Analysis of the Human Cytomegalovirus (HHV5) Genome. Jiri Novotny, Isidore Rigoutsos, David Coleman, Thomas Shenk . JMB, 310, 5, 1151. SEQUENCE ALIGNMENTS, MULTIPLE ALIGNMNETS 27. Pairwise Sequence Alignment Below the Twilight Zone Jonathan D. Blake, Fred E. Cohen , JMB< 307,2, 721. 40. Picasso, Heger, Bioinfo, 17, 3, 272. 26. Consistency Analysis of MUltiple Alignments.... Kunin and Pietrokovski, JMB, 307, 939. MISCELANEOUS: 14. Understanding Hierarchical Protein Evolution from First Principles. Nikolay V. Dokholyan, Eugene I. Shakhnovich . JMB 312, 1, 289. 2. Sequence complexity of disordered protein. Pedro Romero, Zoran Obradovic, Xiaohong Li, Ethan C. Garner, Celeste J. Brown, A. Keith Dunker. Proteins, 42, 1, 38-48. --. Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast Jong Park, Michael Lappe, Sarah A. Teichmann , JMB< 307, 3, 929. PARTIAL LIST OF CS TOPICS COVERED BY THE PAPERS: NP complete problems: 37 String Algorithms: 39 (fractional programming) Linear Programming Optimization: 12 Dynamic Programming: 18 Neural Networks: 2 38 Info. Theory: 2 7 Comput. Geometry: 10 11 18 22 Genetic Algos: 11 Support Vector Machine: 24 35 38 Hidden Markov Models: 32