Articles presented by Alex: __________________________ Magazine: Journal of Computer-Aided Molecular Design 1. ``A review of protein-small molecule docking methods'' R.D. Taylor, P.J. Jewsbury, J.W. Essex J. Comput. Aided Mol. Des. 16 (3): 151-166, March 2002 2. `` Flexible docking under pharmacophore type constraints'' Sally A. Hindle, Matthias Rarey, Christian Buning, Thomas Lengauer J. Comput. Aided Mol. Des. 16 (2): 129-149, February 2002 3. ``Can we separate active from inactive conformations?'' David J. Diller, Kenneth M. Merz, Jr J. Comput. Aided Mol. Des. 16 (2): 105-112, February 2002 4. ``Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools'' Jonas Bostrom J. Comput. Aided Mol. Des. 15 (12): 1137-1152, December 2001 5. ``Structure-based ligand design for flexible proteins: Application of new F-DycoBlock'' Jiang Zhu, Hao Fan, Haiyan Liu, Yunyu Shi J. Comput. Aided Mol. Des. 15 (11): 979-996, November 2001 6. ``A genetic algorithm for structure-based de novo design'' Scott C.-H. Pegg, Jose J. Haresco, Irwin D. Kuntz J. Comput. Aided Mol. Des. 15 (10): 911-933, October 2001 7. ``Functional group placement in protein binding sites: a comparison of GRID and MCSS'' Diane Joseph-McCarthy, James M. Hogle, Martin Karplus J. Comput. Aided Mol. Des. 15 (10): 935-960, October 2001 Articles presented by Oranit: _____________________________ 1. Shoichet BK, McGovern SL, Wei B, Irwin JJ. Lead discovery using molecular docking (Review). Current Opinion in Chemical Biology 6, 439-446 (2002) 2. Alon Efrat, Frank Hoffmann, Klaus Kriegel, Christof Schultz, Carola Wenk: Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels. Journal of Computational Biology 9(2): 299-315 (2002) 3. Nancy M. Amato, Guang Song: Using Motion Planning to Study Protein Folding Pathways. Journal of Computational Biology 9(2): 149-168 (2002) 4. Althaus, E., Kohlbacher, O., Lenhof, H.-P., & Mller, P. A combinatorial approach to protein docking with flexible side-chains. Journal of Computational Biology 9(4): 597-612 (2002) Articles presented by Max: __________________________ 1. Surfacing Signatures: An Orientation Independent Free-Form Surface Representation Scheme for the Purpose of Objects Registration and Matching. Sameh M. Yamany, Aly A. Farag . IEEE Transactions on Pattern Analysis and Machine Intelligence 24(8): 1105-1120 (2002) 2. Z. Aktouf, G. Bertrand, L.Perroton: "A three-dimensional holes closing algorithm", Pattern Recognition Letters, No. 23, pp. 523-531, 2002. 3. A Fourier analysis of symmetry in protein structure. William R. Taylor, Jaap Heringa, Franck Baud, Tomas P. Flores Prot Eng Vol. 15, No. 2, 79-89, February 2002 4. Quantifying the accessible surface area of protein residues in their local enviroment. U. Samanta, R.P. Bahadur, P.Chakrabarti. Prot Eng Vol. 15, No. 8, 659-667, 2002 Articles presented by Dina: ___________________________ PNAS, 2002, vol. 99, 14116-14121 Kortemme T. and Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Protein Engineering, 2002, vol. 15, 669-675 Machicado C. , Bueno M. and Sancho J. Predicting the structure of protein cavities created by mutation. Protein Engineering, 2002, vol. 15, 257-263 Jiang F., Lin W. and Rao Z. SOFTDOCK: understanding of molecular recognition through a systematic docking study. Protein Engineering, 2002, vol. 15, 677-681 Ma XU., Wang CX., Li CH. and Chen WZ. A fast empirical approach to binding free energy calculations based on protein interface information. Protein Engineering, 2002, vol. 15, 279-286 Tosatto S., Bindewald E., Hesser J. and Manner R. A divide and conquer approach to fast loop modeling. Articles presented by Inbal: ___________________________ JMB 2002 324 105-121 Analysis of catalytic residues in enzyme active sites Bartlett, Porter, Borkakoti & Thornton Proteins 2002 48: 439-446 Comparison of sequence and structure alignments for protein domains Marchler-Bauer, Panchenko, Ariel & Bryant Computers & Chemistry 2001 25 329-339 Which craft is best in bioinformatics ? Attwood & Miller