schlauchi's Top Recommendations

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	Drug discovery: a historical perspective. [My Copy] Science, Vol. 287, No. 5460. (17 March 2000), pp. 1960-1964. by J. Drews posted by 18 people jbesnard Yanno BragilMassoud nachtalp kuhn Borelli sangeetha joergkurtwegner jdiggans ramensky Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug LamBras srp33 yaredo
	Protein flexibility in ligand docking and virtual screening to protein kinases. [My Copy] J Mol Biol, Vol. 337, No. 1. (12 March 2004), pp. 209-225. by C. N. Cavasotto, R. A. Abagyan posted by 13 people flbarroso oteri BragilMassoud dgruiz yongzhao sangeetha anwazo daevans kazemi Bioinformatics TSRI_MGL insilicodrug LamBras
	Can Conformational Change Be Described by Only a Few Normal Modes? [My Copy] Biophys. J., Vol. 90, No. 5. (1 March 2006), pp. 1583-1593. by Paula Petrone, Vijay S. Pande posted by 20 people ahmetbakan csrocha BragilMassoud barry dimka aqeel shuns yongzhao xdeupi choonpeng joergkurtwegner daevans structural_bioinformatics Bioinformatics TSRI_MGL Molecular-Modelling Drug-Design Cheminformatics LabCompMed LamBras
	Docking and scoring in virtual screening for drug discovery: methods and applications. [My Copy] Nat Rev Drug Discov, Vol. 3, No. 11. (November 2004), pp. 935-949. by D. B. Kitchen, H. Decornez, J. R. Furr, J. Bajorath posted by 18 people LamBras robert85 BragilMassoud dgruiz beapen anita yongzhao marcius sangeetha Bioinformatics structure-bii TSRI_MGL Atopic_and_Seborrhoeic_Dermatitis Skin_Deep insilicodrug Applied_Bimatics BioinfoCIPF SGU-CIPF
	Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. [My Copy] J Med Chem, Vol. 47, No. 1. (1 January 2004), pp. 45-55. by J. A. Erickson, M. Jalaie, D. H. Robertson, R. A. Lewis, M. Vieth posted by 10 people oteri BragilMassoud apaydin yongzhao sangeetha daevans kazemi Bioinformatics TSRI_MGL insilicodrug
	Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 2. (1 January 2006), pp. 534-553. by Woody Sherman, Tyler Day, Matthew P. Jacobson, Richard A. Friesner, Ramy Farid posted by 9 people klexa sschurer cen4ik LamBras BragilMassoud yongzhao daevans kazemi TSRI_MGL
	Decoys for docking. [My Copy] J Med Chem, Vol. 48, No. 11. (2 June 2005), pp. 3714-3728. by A. P. Graves, R. Brenk, B. K. Shoichet posted by 13 people csrocha oteri simranjeet BragilMassoud dgruiz yongzhao sangeetha insilico blackbart Bioinformatics TSRI_MGL insilicodrug Computer Aided Drug Design
	Virtual screening using protein-ligand docking: avoiding artificial enrichment. [My Copy] J Chem Inf Comput Sci, Vol. 44, No. 3. (n 2004), pp. 793-806. by M. L. Verdonk, V. Berdini, M. J. Hartshorn, et al.W. T. Mooij, C. W. Murray, R. D. Taylor, P. Watson posted by 6 people BragilMassoud nachtalp sangeetha peprovy Bioinformatics insilicodrug
	Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 2. (9 November 2007), pp. 399-421. by Sheng-You Huang, Xiaoqin Zou posted by 11 people nickolay Structural Biology Group TorVergata oteri AliceWang BragilMassoud bicko yongzhao kazemi hmk TSRI_MGL LamBras
	Comparing protein-ligand docking programs is difficult. [My Copy] Proteins (3 June 2005) by Jason C C. Cole, Christopher W W. Murray, J Willem M W. Nissink, Richard D D. Taylor, Robin Taylor posted by 12 people flbarroso BragilMassoud dgruiz thaliana yongzhao sangeetha kzfm peprovy carlescorbi Bioinformatics TSRI_MGL insilicodrug
	Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. [My Copy] Journal of computer-aided molecular design, Vol. 21, No. 5. (27 May 2007), pp. 281-306. by A. N. Jain posted by 7 people vpenelle Structural Biology Group TorVergata oteri BragilMassoud sangeetha Bioinformatics insilicodrug
	Molecular recognition and docking algorithms. [My Copy] Annu Rev Biophys Biomol Struct, Vol. 32 (2003), pp. 335-373. by N. Brooijmans, I. D. Kuntz posted by 11 people flbarroso BragilMassoud yongzhao ttjoseph sangeetha blackbart kazemi massivemayhem Bioinformatics TSRI_MGL insilicodrug
	Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. [My Copy] J Med Chem, Vol. 47, No. 7. (25 March 2004), pp. 1739-1749. by R. A. Friesner, J. L. Banks, R. B. Murphy, et al.T. A. Halgren, J. J. Klicic, D. T. Mainz, M. P. Repasky, E. H. Knoll, M. Shelley, J. K. Perry, D. E. Shaw, P. Francis, P. S. Shenkin posted by 8 people snichols15 flbarroso BragilMassoud dgruiz cantupaz nachtalp LamBras dbougioukou
	Ligand Depot: a data warehouse for ligands bound to macromolecules [My Copy] Bioinformatics, Vol. 20, No. 13. (1 September 2004), pp. 2153-2155. by Zukang Feng, Li Chen, Himabindu Maddula, et al.Ozgur Akcan, Rose Oughtred, Helen M. Berman, John Westbrook posted by 6 people flbarroso reyez BragilMassoud nachtalp bicko nickolay
	Evaluation of library ranking efficacy in virtual screening. [My Copy] J Comput Chem, Vol. 26, No. 1. (15 January 2005), pp. 11-22. by M. Kontoyianni, G. S. Sokol, L. M. McClellan posted by 6 people BragilMassoud nachtalp marcius schuwi BioinfoCIPF SGU-CIPF
	Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance [My Copy] Journal of Medicinal Chemistry, Vol. 50, No. 4. (1 February 2007), pp. 726-741. by Michael J. Hartshorn, Marcel L. Verdonk, Gianni Chessari, et al.Suzanne C. Brewerton, Wijnand T. M. Mooij, Paul N. Mortenson, Christopher W. Murray posted by 10 people flbarroso GermanErlenkamp massivemayhem higueruelo BragilMassoud daevans ramensky hmk superpyrin thanatos
	Assessing scoring functions for protein-ligand interactions. [My Copy] J Med Chem, Vol. 47, No. 12. (3 June 2004), pp. 3032-3047. by P. Ferrara, H. Gohlke, D. J. Price, G. Klebe, C. L. Brooks posted by 4 people oteri AliceWang BragilMassoud nachtalp
	Automatic and Efficient Decomposition of Two-Dimensional Structures of Small Molecules for Fragment-Based High-Throughput Docking. [My Copy] J Med Chem, Vol. 49, No. 25. (14 December 2006), pp. 7384-7392. by Peter Kolb, Amedeo Caflisch posted by 3 people BragilMassoud nachtalp daevans
	Modeling Water Molecules in Protein-Ligand Docking Using GOLD. [My Copy] J Med Chem, Vol. 48, No. 20. (6 October 2005), pp. 6504-6515. by M. L. Verdonk, G. Chessari, J. C. Cole, et al.M. J. Hartshorn, C. W. Murray, J. W. Nissink, R. D. Taylor, R. Taylor posted by 6 people BragilMassoud sangeetha trmr superpyrin Bioinformatics insilicodrug
	Comparison of automated docking programs as virtual screening tools. [My Copy] J Med Chem, Vol. 48, No. 4. (24 February 2005), pp. 962-976. by M. D. Cummings, R. L. DesJarlais, A. C. Gibbs, V. Mohan, E. P. Jaeger posted by 7 people BragilMassoud yongzhao sangeetha kazemi Bioinformatics TSRI_MGL insilicodrug
	Principles of docking: An overview of search algorithms and a guide to scoring functions. [My Copy] Proteins, Vol. 47, No. 4. (1 June 2002), pp. 409-443. by Inbal Halperin, Buyong Ma, Haim Wolfson, Ruth Nussinov posted by 30 people rabio ucbcjbm flbarroso csrocha Structural Biology Group TorVergata oteri timg dgruiz cantupaz apaydin bicko chad_davis yongzhao ttjoseph nickolay ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Bioinformatics TSRI_MGL insilicodrug Evangelia nigham
	Representing receptor flexibility in ligand docking through relevant normal modes. [My Copy] J Am Chem Soc, Vol. 127, No. 26. (6 July 2005), pp. 9632-9640. by C. N. Cavasotto, J. A. Kovacs, R. A. Abagyan posted by 10 people BragilMassoud apaydin barry aqeel yongzhao kazemi structural_bioinformatics Bioinformatics TSRI_MGL LamBras
	Integrating molecular design resources within modern drug discovery research: the Roche experience. [My Copy] Drug Discov Today, Vol. 11, No. 7-8. (April 2006), pp. 326-333. by M. Stahl, W. Guba, M. Kansy posted by 5 people klexa JALumley sschurer BragilMassoud daevans
	Ligand-Protein Docking with Water Molecules [My Copy] J. Chem. Inf. Model. (23 January 2008) by B. C. Roberts, R. L. Mancera posted by 3 people BragilMassoud daevans middledomain
	Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. [My Copy] Protein science : a publication of the Protein Society, Vol. 14, No. 4. (April 2005), pp. 1104-1114. by M. I. Zavodszky, L. A. Kuhn posted by 12 people fl ramensky BragilMassoud dgruiz yongzhao nknii blackbart kazemi rsantana TCR_Signaling TSRI_MGL LamBras
	Toward High-Resolution de Novo Structure Prediction for Small Proteins [My Copy] Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871. by Philip Bradley, Kira M. S. Misura, David Baker posted by 16 people ucbcjbm paddydu kgutwin BragilMassoud ana barry thaliana jwm vavi marcius gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	SODOCK: Swarm optimization for highly flexible protein-ligand docking. [My Copy] J Comput Chem, Vol. 28, No. 2. (30 January 2007), pp. 612-623. by H. M. Chen, B. F. Liu, H. L. Huang, S. F. Hwang, S. Y. Ho posted by 6 people npt11tpn oteri BragilMassoud dgruiz yongzhao TSRI_MGL
	Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screen. [My Copy] Science, Vol. 286, No. 5441. (29 October 1999), pp. 971-974. by T. U. Mayer, T. M. Kapoor, S. J. Haggarty, R. W. King, S. L. Schreiber, T. J. Mitchison posted by 3 people BragilMassoud nachtalp jarasch
	Chemical genetics: tailoring tools for cell biology. [My Copy] Trends Cell Biol, Vol. 13, No. 5. (May 2003), pp. 270-277. by T. U. Mayer posted by 3 people BragilMassoud nachtalp jarasch
	Robust ligand-based modeling of the biological targets of known drugs. [My Copy] Journal of medicinal chemistry, Vol. 49, No. 10. (18 May 2006), pp. 2921-2938. by Ann E. Cleves, Ajay N. Jain posted by 5 people fernan mnishimu BragilMassoud nachtalp jarasch
	Protein-ligand docking: Current status and future challenges [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 1. (21 July 2006), pp. 15-26. by Sérgio F. Sousa, Pedro A. Fernandes, Maria J. Ramos posted by 14 people rabio flbarroso ramensky BragilMassoud yongzhao peprovy kazemi sergio_fms carlescorbi TSRI_MGL robert boris_aguilar qaiser_fatmi Chang group
	Of molecules and humans. [My Copy] J Med Chem, Vol. 49, No. 22. (2 November 2006), pp. 6429-6434. by J. Gasteiger posted by 3 people BragilMassoud nachtalp jarasch
	How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding. [My Copy] J Mol Biol (29 September 2006) by Kannan Gunasekaran, Ruth Nussinov posted by 12 people aqeel reyez BragilMassoud dgruiz radestock lna yongzhao choonpeng TSRI_MGL weisblum higueruelo nickolay
	Global mapping of pharmacological space [My Copy] Nature Biotechnology, Vol. 24, No. 7. (13 July 2006), pp. 805-815. by Gaia V. Paolini, Richard H. B. Shapland, Willem P. van Hoorn, Jonathan S. Mason, Andrew L. Hopkins posted by 14 people bertelsen sameersoi superpyrin richardbickerton ramensky Yanno BragilMassoud guhjy kuhn bicko caporaso allmensch biomedical-nlp jerome_ucsf_slb
	Benchmarking Sets for Molecular Docking [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 23. (1 November 2006), pp. 6789-6801. by Niu Huang, Brian K. Shoichet, John J. Irwin posted by 6 people GermanErlenkamp ihaque BragilMassoud yongzhao daevans TSRI_MGL
	Binding MOAD (Mother Of All Databases). [My Copy] Proteins (21 June 2005) by Liegi Hu, Mark L L. Benson, Richard D D. Smith, Michael G G. Lerner, Heather A A. Carlson posted by 16 people BragilMassoud sangeetha shantanu caporaso papatonyhill structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology biomedical-nlp insilicodrug higueruelo
	A semiempirical free energy force field with charge-based desolvation [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (1 February 2007), pp. 1145-1152. by Ruth Huey, Garrett M. Morris, Arthur J. Olson, David S. Goodsell posted by 8 people trishul nickolay joule Structural Biology Group TorVergata oteri IrinaMoreira BragilMassoud carlescorbi
	Hierarchical and multi-resolution representation of protein flexibility. [My Copy] Bioinformatics (18 September 2006) by Yong Zhao, Daniel Stoffler, Michel Sanner posted by 6 people BragilMassoud dgruiz yongzhao kazemi TSRI_MGL LamBras
	Navigating chemical space for biology and medicine [My Copy] Nature, Vol. 432, No. 7019. (15 December 2004), pp. 855-861. by Christopher Lipinski, Andrew Hopkins posted by 17 people TimRooney nicklynch sameersoi NaCTeM Effie LamBras BragilMassoud kuhn jxl marcius caporaso blackbart EC biomedical-nlp BioinfoCIPF SGU-CIPF jerome_ucsf_slb
	Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes [My Copy] J. Med. Chem. (23 September 2006) by R. A. Friesner, R. B. Murphy, M. P. Repasky, et al.L. L. Frye, J. R. Greenwood, T. A. Halgren, P. C. Sanschagrin, D. T. Mainz posted by 7 people snichols15 flbarroso BragilMassoud dgruiz daevans LamBras middledomain
	A brief history of novel drug discovery technologies. [My Copy] Nat Rev Drug Discov, Vol. 2, No. 4. (April 2003), pp. 321-327. by L. J. Gershell, J. H. Atkins posted by 2 people BragilMassoud nachtalp
	Protein Structure Comparison by Alignment of Distance Matrices [My Copy] Journal of Molecular Biology, Vol. 233, No. 1. (1 September 1993), pp. 123-138. by L. Holm posted by 11 people parnell jwm tjimenez BragilMassoud ana nigham dgront siebertm structural_bioinformatics Bioinformatics sim82
	FlexX-Scan: Fast, structure-based virtual screening [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 57, No. 3. (15 November 2004), pp. 504-517. by Ingo Schellhammer, Matthias Rarey posted by 3 people kaliif BragilMassoud nachtalp
	MolDock: A New Technique for High-Accuracy Molecular Docking. [My Copy] J Med Chem, Vol. 49, No. 11. (1 June 2006), pp. 3315-3321. by R. Thomsen, M. H. Christensen posted by 5 people rsantana oteri BragilMassoud yongzhao TSRI_MGL
	New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities [My Copy] Journal of Computational Chemistry, Vol. 17, No. 9. (7 December 1998), pp. 1132-1141. by Arnaud Blondel, Martin Karplus posted by 2 people BragilMassoud nachtalp
	Using quaternions to calculate RMSD. [My Copy] J Comput Chem, Vol. 25, No. 15. (30 November 2004), pp. 1849-1857. by E. A. Coutsias, C. Seok, K. A. Dill posted by 7 people eskay Diego_Prada BragilMassoud apaydin nachtalp dgront rabio
	Ligand-protein docking using a quantum stochastic tunneling optimization method. [My Copy] J Comput Chem, Vol. 25, No. 6. (30 April 2004), pp. 858-864. by R. L. Mancera, P. Källblad, N. P. Todorov posted by 2 people BragilMassoud nachtalp
	Automated drawing of structural molecular formulas under constraints. [My Copy] J Chem Inf Comput Sci, Vol. 44, No. 3. (n 2004), pp. 1065-1078. by P. C. Fricker, M. Gastreich, M. Rarey posted by 2 people BragilMassoud nachtalp
	The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. [My Copy] J Med Chem, Vol. 47, No. 12. (3 June 2004), pp. 2977-2980. by R. Wang, X. Fang, Y. Lu, S. Wang posted by 2 people BragilMassoud nachtalp
	Structure-based virtual screening of chemical libraries for drug discovery. [My Copy] Curr Opin Chem Biol, Vol. 10, No. 3. (June 2006), pp. 194-202. by S. Ghosh, A. Nie, J. An, Z. Huang posted by 4 people oteri BragilMassoud yongzhao TSRI_MGL
	Can we rationally design promiscuous drugs? [My Copy] Current Opinion in Structural Biology, Vol. 16, No. 1. (24 February 2006), pp. 127-136. by A. Hopkins, J. Mason, J. Overington posted by 11 people pablocarb pauldobson ubcg08l BragilMassoud apaydin kuhn bicko yongzhao TSRI_MGL ramensky aheilbut
	Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. [My Copy] J Med Chem, Vol. 48, No. 13. (30 June 2005), pp. 4432-4443. by X. Barril, S. D. Morley posted by 7 people BragilMassoud apaydin barry yongzhao structural_bioinformatics Bioinformatics TSRI_MGL
	Analysis of domain motions by approximate normal mode calculations [My Copy] Proteins: Structure, Function, and Genetics, Vol. 33, No. 3. (9 March 1999), pp. 417-429. by Konrad Hinsen posted by 9 people abovell BragilMassoud barry shadowman aqeel yongzhao structural_bioinformatics Bioinformatics TSRI_MGL
	The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. [My Copy] Science (New York, N.Y.), Vol. 313, No. 5795. (29 September 2006), pp. 1929-1935. by Justin Lamb, Emily D. Crawford, David Peck, et al.Joshua W. Modell, Irene C. Blat, Matthew J. Wrobel, Jim Lerner, Jean-Philippe P. Brunet, Aravind Subramanian, Kenneth N. Ross, Michael Reich, Haley Hieronymus, Guo Wei, Scott A. Armstrong, Stephen J. Haggarty, Paul A. Clemons, Ru Wei, Steven A. Carr, Eric S. Lander, Todd R. Golub posted by 40 people ilyashl gbloeb zufar ipark-kaist bertelsen mingzhi AbnerCYH Dulcinea dansullivanblk BragilMassoud guhjy kuhn jfr yas balajis marcius lhonigberg neveaire kengg ealloza koller mlovell jdiggans ezra jeremymiller frohike massivemayhem lp2 pablomendes Biostatistics Computational-Genomics Bioinformatics Neuroscience T_lab BioinfoCIPF SGU-CIPF GeschwindLab Plantandetc jdiezperezj askrajiv
	Electrostatics calculations: latest methodological advances. [My Copy] Current opinion in structural biology, Vol. 16, No. 2. (13 April 2006), pp. 142-151. by Patrice Koehl posted by 8 people oteri r2s2 flbarroso LamBras BragilMassoud qwermish RamuAnandakrishnan jteyra
	Integration of virtual and high-throughput screening. [My Copy] Nat Rev Drug Discov, Vol. 1, No. 11. (November 2002), pp. 882-894. by J. Bajorath posted by 6 people jerome BragilMassoud sangeetha Bioinformatics insilicodrug sithmein
	Comparison of Topological, Shape, and Docking Methods in Virtual Screening [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 4. (1 July 2007), pp. 1504-1519. by Georgia B. McGaughey, Robert P. Sheridan, Christopher I. Bayly, et al.J. Chris Culberson, Constantine Kreatsoulas, Stacey Lindsley, Vladimir Maiorov, Jean-Francois Truchon, Wendy D. Cornell posted by 9 people kaliif LamBras BragilMassoud daevans steff83 Computer Aided Drug Design middledomain ucbcjbm thanatos
	Surrogate docking: structure-based virtual screening at high throughput speed. [My Copy] J Comput Aided Mol Des (16 November 2005), pp. 1-15. by Sukjoon Yoon, Andrew Smellie, David Hartsough, Anton Filikov posted by 4 people BragilMassoud sangeetha Bioinformatics insilicodrug
	A new test set for validating predictions of protein-ligand interaction. [My Copy] Proteins, Vol. 49, No. 4. (1 December 2002), pp. 457-471. by J. W. Nissink, C. Murray, M. Hartshorn, M. L. Verdonk, J. C. Cole, R. Taylor posted by 6 people flbarroso BragilMassoud yongzhao blackbart ramensky TSRI_MGL
	DrugScore(CSD)-Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction. [My Copy] J Med Chem, Vol. 48, No. 20. (6 October 2005), pp. 6296-6303. by Hans F. Velec, Holger Gohlke, Gerhard Klebe posted by 6 people BragilMassoud apostola yongzhao insilico ucbcjbm TSRI_MGL
	Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. [My Copy] Proteins, Vol. 43, No. 2. (1 May 2001), pp. 217-226. by Y. Z. Chen, D. G. Zhi posted by 4 people BragilMassoud sangeetha Bioinformatics insilicodrug
	ConsDock: A new program for the consensus analysis of protein-ligand interactions. [My Copy] Proteins, Vol. 47, No. 4. (1 June 2002), pp. 521-533. by N. Paul, D. Rognan posted by 4 people BragilMassoud sangeetha Bioinformatics insilicodrug
	Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. [My Copy] J Med Chem, Vol. 43, No. 25. (14 December 2000), pp. 4759-4767. by C. Bissantz, G. Folkers, D. Rognan posted by 4 people BragilMassoud sangeetha Bioinformatics insilicodrug
	Multiple active site corrections for docking and virtual screening. [My Copy] J Med Chem, Vol. 47, No. 1. (1 January 2004), pp. 80-89. by G. P. Vigers, J. P. Rizzi posted by 4 people BragilMassoud sangeetha Bioinformatics insilicodrug
	TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time. [My Copy] J Comput Aided Mol Des (9 February 2007) by Ingo Schellhammer, Matthias Rarey posted by 5 people BragilMassoud sangeetha peprovy Bioinformatics insilicodrug
	On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 4. (13 February 2006), pp. 892-906. by Murad Nayal, Barry Honig posted by 8 people ubcg08l iaolier BragilMassoud pansapiens tjimenez Einat nickolay structural_bioinformatics
	Receptor flexibility in de novo ligand design and docking. [My Copy] J Med Chem, Vol. 48, No. 21. (20 October 2005), pp. 6585-6596. by I. L. Alberts, N. P. Todorov, P. M. Dean posted by 6 people BragilMassoud dgruiz apaydin yongzhao kazemi TSRI_MGL
	PMF Scoring Revisited [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 20. (1 October 2006), pp. 5895-5902. by Ingo Muegge posted by 4 people nickolay ucbcjbm BragilMassoud peprovy
	Critical assessment of the automated AutoDock as a new docking tool for virtual screening. [My Copy] Proteins (20 September 2006) by Hwangseo Park, Jinuk Lee, Sangyoub Lee posted by 5 people BragilMassoud dgruiz yongzhao insilico TSRI_MGL
	The maximal affinity of ligands. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 18. (31 August 1999), pp. 9997-10002. by I. D. Kuntz, K. Chen, K. A. Sharp, P. A. Kollman posted by 7 people higueruelo ubcg08l bicko pslee BragilMassoud alexg superpyrin
	Empirical force fields for biological macromolecules: overview and issues. [My Copy] Journal of computational chemistry, Vol. 25, No. 13. (1 October 2004), pp. 1584-1604. by A. D. Mackerell posted by 12 people krapnik flbarroso Jiang Research Group whitead BragilMassoud marcius dgront loison mirzazadeh BioinfoCIPF SGU-CIPF AndreaColetta
	Evaluation of docking performance: comparative data on docking algorithms. [My Copy] J Med Chem, Vol. 47, No. 3. (29 January 2004), pp. 558-565. by M. Kontoyianni, L. M. McClellan, G. S. Sokol posted by 11 people oteri yongzhao marcius sangeetha insilico schuwi Bioinformatics TSRI_MGL insilicodrug BioinfoCIPF SGU-CIPF
	QXP: powerful, rapid computer algorithms for structure-based drug design. [My Copy] J Comput Aided Mol Des, Vol. 11, No. 4. (July 1997), pp. 333-344. by C. McMartin, R. S. Bohacek posted by 4 people flbarroso Structural Biology Group TorVergata oteri BragilMassoud
	An ant algorithm for the conformational analysis of flexible molecules [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA. by Frits Daeyaert, Marc De Jonge, Luc Koymans, Maarten Vinkers posted by 8 people npt11tpn BragilMassoud gane5h samjlord rsantana jwagoner superpyrin moernerlab
	MaxSub: an automated measure for the assessment of protein structure prediction quality. [My Copy] Bioinformatics, Vol. 16, No. 9. (September 2000), pp. 776-785. by N. Siew, A. Elofsson, L. Rychlewski, D. Fischer posted by 9 people sebk rabio granujilla BragilMassoud marcius dgront BioinfoCIPF SGU-CIPF biehl
	Validation and use of the MM-PBSA approach for drug discovery. [My Copy] J Med Chem, Vol. 48, No. 12. (16 June 2005), pp. 4040-4048. by B. Kuhn, P. Gerber, T. Schulz-Gasch, M. Stahl posted by 6 people BragilMassoud apostola mleis gcaltabiano LabCompMed LamBras
	A distance geometry heuristic for expanding the range of geometries sampled during conformational search. [My Copy] J Comput Chem (10 October 2006) by Sergei Izrailev, Fangqiang Zhu, Dimitris K K. Agrafiotis posted by 3 people BragilMassoud superpyrin mijam
	Improving binding mode predictions by docking into protein-specifically adapted potential fields. [My Copy] J Med Chem, Vol. 48, No. 17. (25 August 2005), pp. 5466-5479. by S. Radestock, M. Böhm, H. Gohlke posted by 5 people BragilMassoud yongzhao kazemi naitsabes TSRI_MGL
	Docking small-molecule ligands into active sites. [My Copy] Curr Opin Biotechnol, Vol. 6, No. 6. (December 1995), pp. 652-656. by G. Jones, P. Willett posted by 4 people BragilMassoud sangeetha Bioinformatics insilicodrug
	Self-organizing superimposition algorithm for conformational sampling. [My Copy] J Comput Chem (13 February 2007) by Fangqiang Zhu, Dimitris K K. Agrafiotis posted by 2 people BragilMassoud superpyrin
	ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 3. (13 September 2006), pp. 538-548. by Jens Meiler, David Baker posted by 6 people mijam BragilMassoud kuhn jwm yongzhao TSRI_MGL
	Effective handling of induced-fit motion in flexible docking. [My Copy] Proteins (10 March 2006) by Miho Yamada Y. Mizutani, Yoshihiro Takamatsu, Tazuko Ichinose, Kensuke Nakamura, Akiko Itai posted by 4 people BragilMassoud yongzhao kazemi TSRI_MGL
	Searching for functional sites in protein structures. [My Copy] Current opinion in chemical biology, Vol. 8, No. 1. (February 2004), pp. 3-7. by S. Jones, J. M. Thornton posted by 9 people qluo BragilMassoud LeightonP chrn Einat proteasome structural_bioinformatics nickolay jwm
	Progress toward virtual screening for drug side effects. [My Copy] Proteins, Vol. 48, No. 4. (1 September 2002), pp. 664-671. by W. M. Rockey, A. H. Elcock posted by 4 people BragilMassoud sangeetha Bioinformatics insilicodrug
	How to do an evaluation: pitfalls and traps. [My Copy] J Comput Aided Mol Des (23 January 2008) by Paul C. Hawkins, Gregory L. Warren, A G. Skillman, Anthony Nicholls posted by 5 people JALumley massivemayhem BragilMassoud LamBras thanatos
	FLIPDock: Docking flexible ligands into flexible receptors [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 3. (23 May 2007), pp. 726-737. by Yong Zhao, Michel F. Sanner posted by 9 people npt11tpn fl karinaecomp BragilMassoud yongzhao kazemi somak TSRI_MGL LamBras
	Further development and validation of empirical scoring functions for structure-based binding affinity prediction. [My Copy] J Comput Aided Mol Des, Vol. 16, No. 1. (January 2002), pp. 11-26. by R. Wang, L. Lai, S. Wang posted by 3 people BragilMassoud yongzhao TSRI_MGL
	Building-block approach for determining low-frequency normal modes of macromolecules. [My Copy] Proteins, Vol. 41, No. 1. (1 October 2000), pp. 1-7. by F. Tama, F. X. Gadea, O. Marques, Y. H. Sanejouand posted by 5 people BragilMassoud apaydin aqeel yongzhao TSRI_MGL
	Progressive Docking: A Hybrid QSAR/Docking Approach for Accelerating In Silico High Throughput Screening. [My Copy] J Med Chem, Vol. 49, No. 25. (14 December 2006), pp. 7466-7478. by Artem Cherkasov, Fuqiang Ban, Yvonne Li, Magid Fallahi, Geoffrey L. Hammond posted by 3 people BragilMassoud yongzhao TSRI_MGL
	Gradient tabu search. [My Copy] J Comput Chem, Vol. 28, No. 2. (30 January 2007), pp. 601-611. by S. Stepanenko, B. Engels posted by 3 people BragilMassoud yongzhao TSRI_MGL
	Structure alignment via Delaunay tetrahedralization. [My Copy] Proteins (26 April 2005) by Jeffrey Roach, Shantanu Sharma, Maryna Kapustina, Charles W W. Carter posted by 13 people MuraLab BragilMassoud ana barry shantanu structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
	Prediction of Protein-Ligand Interactions. Docking and Scoring: Successes and Gaps. [My Copy] J Med Chem, Vol. 49, No. 20. (5 October 2006), pp. 5851-5855. by Andrew R. Leach, Brian K. Shoichet, Catherine E. Peishoff posted by 5 people ucbcjbm BragilMassoud dgruiz kazemi massivemayhem
	An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. [My Copy] J Chem Inf Comput Sci, Vol. 44, No. 6. (c 2004), pp. 2114-2125. by R. Wang, Y. Lu, X. Fang, S. Wang posted by 3 people BragilMassoud yongzhao TSRI_MGL
	Rapid computational identification of the targets of protein kinase inhibitors. [My Copy] J Med Chem, Vol. 48, No. 12. (16 June 2005), pp. 4138-4152. by W. M. Rockey, A. H. Elcock posted by 3 people BragilMassoud tjimenez apostola
	Protein families and their evolution-a structural perspective. [My Copy] Annu Rev Biochem, Vol. 74 (2005), pp. 867-900. by C. A. Orengo, J. M. Thornton posted by 27 people krapnik dfdong ucbcjbm flbarroso kumar_physics yuslinaz ssgong ana barry tjimenez jwm chad_davis Einat Schmidtc marcius sriram_s ezotenko redelings medic0747 structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF nigham sim82
	Bayesian Network Classifiers [My Copy] Machine Learning, Vol. 29, No. 2-3. (1997), pp. 131-163. by Nir Friedman, Dan Geiger, Moises Goldszmidt posted by 5 people BragilMassoud barry dliu structural_bioinformatics Bioinformatics
	Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. [My Copy] Biophys J (6 May 2005) by Wenjun Zheng, Bernard R R. Brooks posted by 8 people BragilMassoud barry baaden aqeel shuns qwermish structural_bioinformatics Bioinformatics
	Coarse-grained normal mode analysis in structural biology [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 5. (October 2005), pp. 586-592. by Ivet Bahar, Aj Rader posted by 10 people BragilMassoud apaydin barry aqeel shuns scis0000001 insectopalo structural_bioinformatics Bioinformatics higueruelo
	Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. [My Copy] J Comput Aided Mol Des, Vol. 16, No. 12. (December 2002), pp. 883-902. by M. I. Zavodszky, P. C. Sanschagrin, R. S. Korde, L. A. Kuhn posted by 3 people BragilMassoud nickolay blackbart
	Flexible protein–protein docking [My Copy] Current Opinion in Structural Biology In Theory and simulation/Macromolecular assemblages - Joel Janin and Michael Levitt/Edward H Egelman and Andrew GW Leslie, Vol. 16, No. 2. (April 2006), pp. 194-200. by A BONVIN, posted by 16 people rabio timg flbarroso oteri laurabailey dgruiz aqeel bicko yongzhao ima sangeetha gloria Bioinformatics TSRI_MGL insilicodrug higueruelo