daevans'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
	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
	GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein-Ligand Complexes. [My Copy] J Chem Inf Model, Vol. 47, No. 4. (g 2007), pp. 1657-1672. by S. Tietze, J. Apostolakis posted by 4 people klexa BragilMassoud schlauchi sim82
	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
	Docking small ligands in flexible binding sites [My Copy] Journal of Computational Chemistry, Vol. 19, No. 1. (1998), pp. 21-37. by Joannis Apostolakis, Andreas Plückthun, Amedeo Caflisch posted by 4 people karinaecomp klexa BragilMassoud schlauchi
	Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 1. (1 January 2007), pp. 195-207. by Gilles Marcou, Didier Rognan posted by 9 people RebeccaHamer klexa richardbickerton nanonan BragilMassoud peprovy schlauchi massivemayhem sithmein
	Comparative evaluation of eight docking tools for docking and virtual screening accuracy. [My Copy] Proteins, Vol. 57, No. 2. (1 November 2004), pp. 225-242. by E. Kellenberger, J. Rodrigo, P. Muller, D. Rognan posted by 8 people klexa oteri BragilMassoud dgruiz sangeetha schlauchi Bioinformatics insilicodrug
	FINDSITE<sup>LHM</sup>: A Threading-Based Approach to Ligand Homology Modeling [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (5 June 2009), e1000405. by Michal Brylinski, Jeffrey Skolnick posted by 9 people phoenixzxl nickolay kshameer superpyrin reyez apaydin structural_bioinformatics McCammon barry
	Structure-based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections. [My Copy] Proteins, Vol. 68, No. 3. (15 August 2007), pp. 712-725. by M. Montes, M. A. Miteva, B. O. Villoutreix posted by 2 people klexa schlauchi
	Predicting substrates by docking high-energy intermediates to enzyme structures. [My Copy] J Am Chem Soc, Vol. 128, No. 49. (13 December 2006), pp. 15882-15891. by J. C. Hermann, E. Ghanem, Y. Li, F. M. Raushel, J. J. Irwin, B. K. Shoichet posted by 2 people klexa schlauchi
	The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. [My Copy] J Comput Aided Mol Des, Vol. 13, No. 6. (November 1999), pp. 547-562. by C. W. Murray, C. A. Baxter, A. D. Frenkel posted by 2 people klexa schlauchi
	Flexible protein-ligand docking by global energy optimization in internal coordinates [My Copy] Proteins: Structure, Function, and Genetics, Vol. 29, No. S1. (1997), pp. 215-220. by Maxim Totrov, Ruben Abagyan posted by 2 people klexa schlauchi
	An introduction to ROC analysis [My Copy] Pattern Recogn. Lett. In ROC Analysis in Pattern Recognition, Vol. 27, No. 8. (June 2006), pp. 861-874. by Tom Fawcett posted by 43 people JALumley singhsh TLVincent module qluo q_w_e_r_t_y makrehchi Borelli mthomure sbarthelme jjrodriguez cen4ik jmetzen MosesCheckley ldietz vavi dquest sdvillal xiaoyan2006 dwf camu schlauchi vmoa drivard nklee imrchen kmdaily gsiwo Bioinformatics Crypto VT_DLRL Randomness LIVIA tgyork idonaldson BergmanLab napvasconcelos cdeane haiyeong AbnerCYH isimpson guhjy nherveg
	Optimal docking area: a new method for predicting protein-protein interaction sites. [My Copy] Proteins, Vol. 58, No. 1. (1 January 2005), pp. 134-143. by J. Fernandez-Recio, M. Totrov, C. Skorodumov, R. Abagyan posted by 8 people klexa jwm bicko schlauchi cjeans Radiation_Damage Stressosome marti
	A review of protein-small molecule docking methods. [My Copy] J Comput Aided Mol Des, Vol. 16, No. 3. (March 2002), pp. 151-166. by R. D. Taylor, P. J. Jewsbury, J. W. Essex posted by 12 people klexa csrocha Structural Biology Group TorVergata oteri marcius sangeetha schlauchi massivemayhem Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
	DRUG RESEARCH: MYTHS, HYPE AND REALITY [My Copy] Nat Rev Drug Discov, Vol. 2, No. 8. (2003), pp. 665-668. by Hugo Kubinyi posted by 6 people joergkurtwegner massivemayhem Molecular-Modelling Drug-Design Cheminformatics LamBras
	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
	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
	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
	RASCAL: Calculation of Graph Similarity using Maximum Common Edge Subgraphs [My Copy] The Computer Journal, Vol. 45, No. 6. (1 June 2002), pp. 631-644. by John W. Raymond, Eleanor J. Gardiner, Peter Willett posted by 8 people BragilMassoud schlauchi koerner jarasch simons noby superpyrin jcrab
	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
	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
	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
	Computational methods for the structural alignment of molecules. [My Copy] J Comput Aided Mol Des, Vol. 14, No. 3. (March 2000), pp. 215-232. by C. Lemmen, T. Lengauer posted by 5 people BragilMassoud tjimenez nachtalp schlauchi superpyrin
	A fast flexible docking method using an incremental construction algorithm. [My Copy] J Mol Biol, Vol. 261, No. 3. (23 August 1996), pp. 470-489. by M. Rarey, B. Kramer, T. Lengauer, G. Klebe posted by 5 people BragilMassoud tjimenez nachtalp schlauchi superpyrin
	Conformational Diversity of Ligands Bound to Proteins [My Copy] Journal of Molecular Biology, Vol. 356, No. 4. (3 March 2006), pp. 928-944. by Gareth R. Stockwell, Janet M. Thornton posted by 8 people JALumley ubcg08l BragilMassoud apaydin kuhn bilab grottenolm 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
	Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein-Ligand Complexes. [My Copy] J Chem Inf Model (1 February 2007) by Yipin Lu, Renxiao Wang, Chao-Yie Y. Yang, Shaomeng Wang posted by 3 people npt11tpn BragilMassoud LamBras
	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
	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
	High-throughput drug discovery: what can we expect from HTS? [My Copy] Drug Discov Today, Vol. 10, No. 1. (1 January 2005), pp. 17-22. by P. Gribbon, A. Sewing posted by 2 people LamBras BragilMassoud
	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
	Data mining and machine learning techniques for the identification of mutagenicity inducing substructures and structure activity relationships of noncongeneric compounds. [My Copy] J Chem Inf Comput Sci, Vol. 44, No. 4. (g 2004), pp. 1402-1411. by C. Helma, T. Cramer, S. Kramer, L. De Raedt posted by 3 people jxl BragilMassoud LamBras
	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
	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
	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
	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
	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
	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
	Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. [My Copy] J Med Chem, Vol. 47, No. 7. (25 March 2004), pp. 1750-1759. by T. A. Halgren, R. B. Murphy, R. A. Friesner, et al.H. S. Beard, L. L. Frye, W. T. Pollard, J. L. Banks posted by 5 people snichols15 flbarroso BragilMassoud schlauchi LamBras
	Development and validation of a modular, extensible docking program: DOCK 5. [My Copy] J Comput Aided Mol Des (6 December 2006) by Demetri T. Moustakas, P T. Lang, Scott Pegg, et al.Eric Pettersen, Irwin D. Kuntz, Natasja Brooijmans, Robert C. Rizzo posted by 4 people BragilMassoud yongzhao schlauchi TSRI_MGL
	The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. [My Copy] J Comput Aided Mol Des, Vol. 8, No. 3. (June 1994), pp. 243-256. by H. J. Böhm posted by 5 people BragilMassoud nachtalp nickolay papatonyhill schlauchi
	Virtual Screening Workflow Development Guided by the “Receiver Operating Characteristic” Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4 [My Copy] Journal of Medicinal Chemistry, Vol. 48, No. 7. (1 April 2005), pp. 2534-2547. by Nicolas Triballeau, Francine Acher, Isabelle Brabet, Jean-Philippe Pin, Hugues-Olivier Bertrand posted by 5 people JALumley BragilMassoud nachtalp peprovy schlauchi
	Minimizing false positives in kinase virtual screens. [My Copy] Proteins (17 May 2006) by Emanuele Perola posted by 2 people BragilMassoud schlauchi
	Automated docking of substrates to proteins by simulated annealing. [My Copy] Proteins, Vol. 8, No. 3. (1990), pp. 195-202. by D. S. Goodsell, A. J. Olson posted by 5 people joule BragilMassoud apostola robert schlauchi
	Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. [My Copy] Proteins, Vol. 37, No. 2. (1 November 1999), pp. 228-241. by B. Kramer, M. Rarey, T. Lengauer posted by 2 people BragilMassoud schlauchi
	ROCR: visualizing classifier performance in R. [My Copy] Bioinformatics (11 August 2005) by Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer posted by 18 people edvin dfdong natstreet druvus BragilMassoud ana barry Ayest lyongu marcius schlauchi gokhan za structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF bertelsen
	Validation of the general purpose tripos 5.2 force field [My Copy] Journal of Computational Chemistry, Vol. 10, No. 8. (7 September 2004), pp. 982-1012. by Matthew Clark, Richard D. Cramer, Nicole Van Opdenbosch posted by 4 people Gershom BragilMassoud nachtalp schlauchi
	Searching techniques for databases of two- and three-dimensional chemical structures. [My Copy] J Med Chem, Vol. 48, No. 13. (30 June 2005), pp. 4183-4199. by P. Willett posted by 2 people BragilMassoud schlauchi
	Automatic identification and representation of protein binding sites for molecular docking. [My Copy] Protein Sci, Vol. 6, No. 3. (March 1997), pp. 524-533. by J. Ruppert, W. Welch, A. N. Jain posted by 3 people BragilMassoud nachtalp schlauchi
	Development and validation of a genetic algorithm for flexible docking. [My Copy] J Mol Biol, Vol. 267, No. 3. (4 April 1997), pp. 727-748. by G. Jones, P. Willett, R. C. Glen, A. R. Leach, R. Taylor posted by 3 people BragilMassoud nachtalp schlauchi
	Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. [My Copy] J Comput Aided Mol Des, Vol. 11, No. 5. (September 1997), pp. 425-445. by M. D. Eldridge, C. W. Murray, T. R. Auton, G. V. Paolini, R. P. Mee posted by 3 people BragilMassoud nachtalp schlauchi
	A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. [My Copy] Proteins, Vol. 56, No. 2. (1 August 2004), pp. 235-249. by E. Perola, W. P. Walters, P. S. Charifson posted by 9 people oteri ramensky BragilMassoud yongzhao marcius schlauchi TSRI_MGL BioinfoCIPF SGU-CIPF
	Placement of medium-sized molecular fragments into active sites of proteins. [My Copy] J Comput Aided Mol Des, Vol. 10, No. 1. (February 1996), pp. 41-54. by M. Rarey, S. Wefing, T. Lengauer posted by 3 people BragilMassoud tjimenez schlauchi
	Ligand-Based Structural Hypotheses for Virtual Screening [My Copy] J Med Chem In Journal of Medicinal Chemistry, Vol. 47, No. 4. (1 February 2004), pp. 947-961. by Ajay N. Jain posted by 8 people ihaque BragilMassoud nachtalp sangeetha schlauchi jarasch Bioinformatics insilicodrug
	Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. [My Copy] J Med Chem, Vol. 46, No. 4. (13 February 2003), pp. 499-511. by A. N. Jain posted by 6 people oteri BragilMassoud nachtalp yongzhao schlauchi TSRI_MGL
	Classification of kinase inhibitors using a Bayesian model. [My Copy] J Med Chem, Vol. 47, No. 18. (26 August 2004), pp. 4463-4470. by X. Xia, E. G. Maliski, P. Gallant, D. Rogers posted by 4 people jerome kuhn LamBras thanatos
	In Silico Prediction of Cytochrome P450 2D6 and 3A4 Inhibition Using Gaussian Kernel Weighted k-Nearest Neighbor and Extended Connectivity Fingerprints, Including Structural Fragment Analysis of Inhibitors versus Noninhibitors [My Copy] J. Med. Chem., Vol. 50, No. 3. (8 February 2007), pp. 501-511. by B. F. Jensen, C. Vind, S. B. Padkjar, P. B. Brockhoff, H. H. F. Refsgaard posted by 2 people LamBras superpyrin
	Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors [My Copy] Angewandte Chemie International Edition, Vol. 41, No. 15. (2002), pp. 2644-2676. by Holger Gohlke, Gerhard Klebe posted by 4 people kazemi superpyrin LamBras boris_aguilar
	Graph-Based Molecular Alignment (GMA) [My Copy] J. Chem. Inf. Model., Vol. 47, No. 2. (26 March 2007), pp. 591-601. by J. Marialke, R. Korner, S. Tietze, J. Apostolakis posted by 3 people schlauchi superpyrin sim82
	FLAME: A Program to Flexibly Align Molecules [My Copy] J. Chem. Inf. Model., Vol. 46, No. 1. (23 January 2006), pp. 298-306. by S. J. Cho, Y. Sun posted by 2 people schlauchi superpyrin
	FLEXS: a method for fast flexible ligand superposition. [My Copy] J Med Chem, Vol. 41, No. 23. (5 November 1998), pp. 4502-4520. by C. Lemmen, T. Lengauer, G. Klebe posted by 5 people oteri tjimenez nachtalp schlauchi superpyrin
	RigFit: a new approach to superimposing ligand molecules. [My Copy] J Comput Aided Mol Des, Vol. 12, No. 5. (September 1998), pp. 491-502. by C. Lemmen, C. Hiller, T. Lengauer posted by 3 people tjimenez schlauchi superpyrin
	How to get the most out of your curation effort. [My Copy] PLoS computational biology, Vol. 5, No. 5. (22 May 2009), e1000391. by Andrey Rzhetsky, Hagit Shatkay, W. John Wilbur posted by 22 people downer daveGerrard Orengo Group Journal Picks CorinYeats abhishek_tiwari daforerog klexa lptolik kiekyon badger_master baker-group sobolevnrm druvus martingerner BergmanLab cisevol Journal picks AlexBateman VGreiff allysonlister fgibson dullhunk
	Ten Simple Rules for Choosing between Industry and Academia [My Copy] PLoS Computational Biology, Vol. 5, No. 6. (26 June 2009), e1000388. by David B. Searls posted by 48 people isp GustavoLacerda twecker agomez druvus tux2000 leliavski jfr welliegirl Sergey_gerbek cyounkin Tomste Horduna aaltenburger Zephyrus CulCog thegoose Yanno timflutre tnhh PeteField MarcoAlvarez sobolevnrm Bioinformatics - CRUK Stew dbikard jasontsai casutton franklu310 kieran101 chrisamiller rdiaz daveGerrard reyez neils marekrud Borelli psique kshameer gjuggler sdaehne flips Journal picks ppgardne fgibson McCammon barry dullhunk
	Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis [My Copy] PLoS ONE, Vol. 4, No. 5. (13 May 2009), e5525. by Nilesh K. Banavali, Alexander D. Mackerell posted by 4 people McCammon barry baker-group sobolevnrm
	Force Field Bias in Protein Folding Simulations [My Copy] Biophysical Journal, Vol. 96, No. 9. (06 May 2009), pp. 3772-3780. by Peter L. Freddolino, Sanghyun Park, Benoît Roux, Klaus Schulten posted by 2 people McCammon jmccammon
	Development and NMR validation of minimal pharmacophore hypotheses for the generation of fragment libraries enriched in heparanase inhibitors [My Copy] Journal of Computer-Aided Molecular Design, Vol. 23, No. 8. (1 August 2009), pp. 555-569. by Rafael Gozalbes, Silvia Mosulén, Rodrigo Carbajo, Antonio Pineda-Lucena posted by 1 person klexa
	Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation [My Copy] Journal of Computer-Aided Molecular Design, Vol. 23, No. 8. (1 August 2009), pp. 541-554. by Kathryn Loving, Noeris Salam, Woody Sherman posted by 1 person sschurer
	Protein Ionizable Groups: pK Values and Their Contribution to Protein Stability and Solubility [My Copy] Journal of Biological Chemistry, Vol. 284, No. 20. (15 May 2009), pp. 13285-13289. by C. Nick Pace, Gerald R. Grimsley, J. Martin Scholtz posted by 10 people pjkiley scampos klexa nanonan structural_bioinformatics McCammon barry baker-group sobolevnrm paulschlesinger
	Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics-Based Ligand Charges and a Hybrid Water Model [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Debananda Das, Yasuhiro Koh, Yasushi Tojo, Arun K. Ghosh, Hiroaki Mitsuya posted by 1 person klexa
	Accurate Automated Protein NMR Structure Determination Using Unassigned NOESY Data. [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (9 December 2009) by Srivatsan Raman, Yuanpeng J. Huang, Binchen Mao, et al.Paolo Rossi, James M. Aramini, Gaohua Liu, Gaetano T. Montelione, David Baker posted by 2 people apaydin klexa
	Recipes for the Selection of Experimental Protein Conformations for Virtual Screening [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan posted by 1 person klexa
	Protein−Ligand Docking Using Mutually Orthogonal Latin Squares (MOLSDOCK) [My Copy] Journal of Chemical Information and Modeling In Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by S. Nehru Viji, P. Arun Prasad, N. Gautham posted by 2 people klexa ima
	Small-World Phenomena in Chemical Library Networks: Application to Fragment-Based Drug Discovery [My Copy] Journal of Chemical Information and Modeling In Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Naoki Tanaka, Kazuki Ohno, Tatsuya Niimi, Ayako Moritomo, Kenichi Mori, Masaya Orita posted by 2 people klexa ihaque
	High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Simone Sciabola, Robert V. Stanton, James E. Mills, et al.Maria M. Flocco, Massimo Baroni, Gabriele Cruciani, Francesca Perruccio, Jonathan S. Mason posted by 2 people klexa zimbo1
	Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions [My Copy] Journal of Chemical Information and Modeling In Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Sourav Das, Arshad Kokardekar, Curt M. Breneman posted by 3 people klexa stharward nickolay
	Toward a Unified Representation of Protein Structural Dynamics in Solution [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Phineus R. L. Markwick, Guillaume Bouvignies, Loic Salmon, J. Andrew McCammon, Michael Nilges, Martin Blackledge posted by 1 person klexa
	MDLab: A molecular dynamics simulation prototyping environment [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), pp. NA-NA. by Trevor Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesús A. Izaguirre posted by 3 people Structural Biology Group TorVergata oteri klexa
	<I>In silico</I> prediction and screening of gamma-secretase inhibitors by molecular descriptors and machine learning methods [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Xue-Gang Yang, Wei Lv, Yu-Zong Chen, Ying Xue posted by 2 people iskathy klexa
	Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Hisashi Okumura, Emilio Gallicchio, Ronald M. Levy posted by 1 person klexa
	Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 10. (26 October 2009), pp. 2333-2343. by Oranit Dror, Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson posted by 1 person klexa
	OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold [My Copy] Protein Science, Vol. 18, No. 1. (2009), pp. 180-195. by Hossein Fazelinia, Patrick C. Cirino, Costas D. Maranas posted by 1 person klexa
	Efficient nonbonded interactions for molecular dynamics on a graphics processing unit [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Peter Eastman, Vijay S. Pande posted by 2 people klexa RamuAnandakrishnan
	High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (9 October 2009), e1000528. by Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, et al.Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji posted by 8 people paulymer ibuch klexa skywalkerus02 kentsis reyez McCammon barry
	Structure-Based Predictive Models for Allosteric Hot Spots [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (9 October 2009), e1000531. by Omar N. A. Demerdash, Michael D. Daily, Julie C. Mitchell posted by 6 people richardbickerton apaydin nickolay klexa McCammon barry
	Secbase: Database Module To Retrieve Secondary Structure Elements with Ligand Binding Motifs [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Oliver Koch, Jason Cole, Peter Block, Gerhard Klebe posted by 2 people reyez klexa
	Accuracy analysis of multiple structure alignments [My Copy] Protein Science, Vol. 18, No. 10. (October 2009), pp. 2027-2035. by Christoph Berbalk, Christine S. Schwaiger, Peter Lackner posted by 3 people dimka nickolay klexa
	Subtype Polymorphisms Among HIV-1 Protease Variants Confer Altered Flap Conformations and Flexibility [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Jamie L. Kear, Mandy E. Blackburn, Angelo M. Veloro, Ben M. Dunn, Gail E. Fanucci posted by 1 person klexa
	Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (18 September 2009), e1000512. by Rui-Ru Ji, Heshani de Silva, Yisheng Jin, et al.Robert E. Bruccoleri, Jian Cao, Aiqing He, Wenjun Huang, Paul S. Kayne, Isaac M. Neuhaus, Karl-Heinz Ott, Becky Penhallow, Mark I. Cockett, Michael G. Neubauer, Nathan O. Siemers, Petra Ross-Macdonald posted by 4 people klexa mingzhi kshameer giovanni
	Detection of Functional Modes in Protein Dynamics [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000480. by Jochen S. Hub, Bert L. de Groot posted by 5 people paulymer sobolevnrm klexa Diego_Prada zwang
	Computation of Conformational Coupling in Allosteric Proteins [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000484. by Brian A. Kidd, David Baker, Wendy E. Thomas posted by 11 people richardbickerton apaydin skywalkerus02 sobolevnrm klexa oteri boris_aguilar bmduggan McCammon barry zwang
	Pushing structural information into the yeast interactome by high-throughput protein docking experiments. [My Copy] PLoS computational biology, Vol. 5, No. 8. (28 August 2009), e1000490. by Roberto Mosca, Carles Pons, Juan Fernández-Recio, Patrick Aloy posted by 7 people chad_davis klexa Orengo Group Journal Picks bdessailly zwang phoenixzxl TRHvidsten
	Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (21 August 2009), e1000475. by Joost Van Durme, Sebastian Maurer-Stroh, Rodrigo Gallardo, Hannah Wilkinson, Frederic Rousseau, Joost Schymkowitz posted by 3 people klexa pansapiens biomcgary
	A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (21 August 2009), e1000474. by James C. Adams, Michael J. Keiser, Li Basuino, et al.Henry F. Chambers, Deok-Sun Lee, Olaf G. Wiest, Patricia C. Babbitt posted by 11 people richardbickerton sobolevnrm nickolay klexa Orengo Group Journal Picks bdessailly pablocarb ptrobajo biomcgary reyez thomaskelder
	Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (14 August 2009), e1000470. by Mati Cohen, Vladimir Potapov, Gideon Schreiber posted by 9 people wilbur richardbickerton nickolay klexa Diego_Prada zwang reyez TRHvidsten ericrpaquet
	Multiple sequence alignment algorithm based on a dispersion graph and ant colony algorithm [My Copy] Journal of Computational Chemistry, Vol. 30, No. 13. (2009), pp. 2031-2038. by Weiyang Chen, Bo Liao, Wen Zhu, Xuyu Xiang posted by 1 person klexa
	Automated scaffold selection for enzyme design [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. 1. (2009), pp. 74-83. by Christoph Malisi, Oliver Kohlbacher, Birte Höcker posted by 1 person klexa
	Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. 1. (2009), pp. 38-51. by Yelena A. Arnautova, Yury N. Vorobjev, Jorge A. Vila, Harold A. Scheraga posted by 1 person klexa
	Blind docking of 260 protein-ligand complexes with EADock 2.0 [My Copy] Journal of Computational Chemistry, Vol. 30, No. 13. (2009), pp. 2021-2030. by Aurélien Grosdidier, Vincent Zoete, Olivier Michielin posted by 1 person klexa