BragilMassoud's Top Recommendations

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	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
	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 Alexandre M. J. J. Bonvin posted by 15 people timg flbarroso oteri laurabailey dgruiz aqeel bicko yongzhao ima sangeetha gloria Bioinformatics TSRI_MGL insilicodrug higueruelo
	Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function [My Copy] Journal of Computational Chemistry, Vol. 19, No. 14. (6 January 1998), pp. 1639-1662. by Garrett M. Morris, David S. Goodsell, Robert S. Halliday, et al.Ruth Huey, William E. Hart, Richard K. Belew, Arthur J. Olson posted by 25 people nickolay npt11tpn jamalex joule lna Lombardo_7 karinaecomp oteri A_Coletta_Thesis Chang group arlam dgruiz nachtalp P2324548 yongzhao peprovy tovrstra papatonyhill schlauchi carlescorbi TSRI_MGL middledomain LamBras andreramme UVA_mag_res
	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
	Improved side-chain modeling for protein-protein docking. [My Copy] Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339. by C. Wang, O. Schueler-Furman, D. Baker posted by 15 people dgront csrocha barry aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac structural_bioinformatics Bioinformatics TSRI_MGL Evangelia
	The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein-Protein Complexes with an Application to Protein-Protein Docking [My Copy] Journal of Molecular Biology, Vol. 347, No. 5. (15 April 2005), pp. 1077-1101. by Graham R. Smith, Michael Sternberg, Paul A. Bates posted by 10 people ana barry aqeel bicko yongzhao ttjoseph structural_bioinformatics Bioinformatics TSRI_MGL jteyra
	Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. [My Copy] Proteins, Vol. 48, No. 4. (1 September 2002), pp. 682-695. by W. G. Krebs, V. Alexandrov, C. A. Wilson, N. Echols, H. Yu, M. Gerstein posted by 9 people apaydin ana barry aqeel yongzhao martainn structural_bioinformatics Bioinformatics TSRI_MGL
	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
	Combining docking and molecular dynamic simulations in drug design. [My Copy] Med Res Rev (6 June 2006) by Hernán Alonso, Andrey A A. Bliznyuk, Jill E E. Gready posted by 11 people karinaecomp flbarroso hryk Structural Biology Group TorVergata oteri A_Coletta_Thesis aqeel yongzhao kazemi TSRI_MGL LamBras
	Computational Alanine Scanning of Protein-Protein Interfaces [My Copy] Sci. STKE, Vol. 2004, No. 219. (10 February 2004), pl2. by Tanja Kortemme, David E. Kim, David Baker posted by 15 people chemrahul82 onufriev pablocarb bicko barry sangeetha blackbart joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug skoddet
	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 26 people 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
	Virtual Screening against Metalloenzymes for Inhibitors and Substrates. [My Copy] Biochemistry, Vol. 44, No. 37. (20 September 2005), pp. 12316-12328. by J. J. Irwin, F. M. Raushel, B. K. Shoichet posted by 6 people yongzhao sangeetha Bioinformatics TSRI_MGL insilicodrug Evangelia
	Conformational sampling for the impatient. [My Copy] Biophys Chem, Vol. 107, No. 3. (15 February 2004), pp. 213-220. by K. Tai posted by 7 people barry baaden yongzhao dgront structural_bioinformatics Bioinformatics TSRI_MGL
	The Protein Data Bank [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 235-242. by Helen M. Berman, John Westbrook, Zukang Feng, et al.Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne posted by 50 people krapnik barmak7282 viktor21614 badi ucbcjbm TLVincent maria_hauser Martin8223 tomjad Diego_Prada flbarroso Taguan oceanwind dsmueller fisherp semin MarcoAlvarez kumar_physics References for 3DSim paper LamBras RamuAnandakrishnan nlapalu reyez nigham lillekatt thaliana dimka kuhn jwm vavi bicko itmeson dgront caporaso condon aengisch debatebob massivemayhem gisle girschick selrac Radiation_Damage Stressosome biomedical-nlp beta tji higueruelo boris_aguilar sebk timg
	Virtual screening for anti-HIV-1 RT and anti-HIV-1 PR inhibitors from the Thai medicinal plants database: a combined docking with neural networks approach. [My Copy] Comb Chem High Throughput Screen, Vol. 8, No. 5. (August 2005), pp. 417-429. by C. Sangma, D. Chuakheaw, N. Jongkon, et al.K. Saenbandit, P. Nunrium, P. Uthayopas, S. Hannongbua posted by 5 people yongzhao sangeetha Bioinformatics TSRI_MGL insilicodrug
	A low-molecular-weight compound discovered through virtual database screening inhibits Stat3 function in breast cancer cells [My Copy] PNAS, Vol. 102, No. 13. (29 March 2005), pp. 4700-4705. by Hui Song, Renxiao Wang, Shaomeng Wang, Jiayuh Lin posted by 5 people yongzhao sangeetha Bioinformatics TSRI_MGL insilicodrug
	MolMovDB: analysis and visualization of conformational change and structural flexibility. [My Copy] Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 478-482. by N. Echols, D. Milburn, M. Gerstein posted by 10 people barry nigham yongzhao joergkurtwegner structural_bioinformatics Bioinformatics TSRI_MGL Molecular-Modelling Drug-Design Cheminformatics
	Progress in Modeling of Protein Structures and Interactions [My Copy] Science, Vol. 310, No. 5748. (28 October 2005), pp. 638-642. by Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura, David Baker posted by 22 people krapnik rabio ucbcjbm paddydu flbarroso thaliana jwm vavi bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo BioinfoCIPF SGU-CIPF barry structural_bioinformatics
	iGNM: a database of protein functional motions based on Gaussian Network Model. [My Copy] Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 2978-2987. by L. W. Yang, X. Liu, C. J. Jursa, et al.M. Holliman, A. J. Rader, H. A. Karimi, I. Bahar posted by 7 people barry baaden yongzhao choonpeng structural_bioinformatics Bioinformatics TSRI_MGL
	Rotamer libraries in the 21st century. [My Copy] Current opinion in structural biology, Vol. 12, No. 4. (August 2002), pp. 431-440. by Roland L. Dunbrack posted by 11 people bmduggan yongzhao dgront blackbart kazemi rsantana medic0747 TSRI_MGL LamBras mijam jwm
	Hierarchical clustering of the correlation patterns: New method of domain identification in proteins. [My Copy] Biophys Chem (24 August 2005) by S O O. Yesylevskyy, V N N. Kharkyanen, A P P. Demchenko posted by 6 people barry yongzhao choonpeng structural_bioinformatics Bioinformatics TSRI_MGL
	Analysis of domain motions in large proteins [My Copy] Proteins: Structure, Function, and Genetics, Vol. 34, No. 3., pp. 369-382. by Konrad Hinsen, Aline Thomas, Martin J. Field posted by 7 people ubcg08l barry shadowman yongzhao structural_bioinformatics Bioinformatics TSRI_MGL
	MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. [My Copy] Proteins, Vol. 49, No. 3. (15 November 2002), pp. 350-364. by L. Lu, H. Lu, J. Skolnick posted by 12 people ana bicko chad_davis marcius sangeetha ruvido structural_bioinformatics Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF kgutwin
	Data clustering: a review [My Copy] ACM Comput. Surv., Vol. 31, No. 3. (September 1999), pp. 264-323. by A. K. Jain, M. N. Murty, P. J. Flynn posted by 78 people emailhy erikv thegoose elan urvoy stharward thefillm operon avoregnitiv fer votis pick600 pbk nhoussos qwermish svozil takeha-e eabait mthomure mercutio egh ericyu karbak dgruiz pdlug thsant mapio mhay davidbrooks imouthesmp dfrankow rahul marcius stagediver sterovetta sangeetha chadhogg sdvillal dgront styliani alexhofmann gane5h ianturton bigbossman perceptron allmensch aviad_work julianpan atbrew sugarexpletive KillianKay mkolar sajan dvisoin theodora jcsilva furykerry koles video_retrieval kdl GroupLens Bioinformatics SRL insilicodrug BioinfoCIPF SGU-CIPF MScResearchRessources NDSiTransitRessources NDS106ProjectRessources NDSIntraVehicularResearch ahat Community_SSTZ paulovn AbnerCYH tnhh flaviovdf dragonrez iraklis
	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 Douglas B. Kitchen, Helene Decornez, John R. Furr, Jurgen Bajorath posted by 8 people Lombardo_7 LamBras sangeetha blackbart schlauchi Bioinformatics insilicodrug mingzhi
	Scalable molecular dynamics with NAMD [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (December 2005), pp. 1781-1802. by James C. Phillips, Rosemary Braun, Wei Wang, et al.James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten posted by 26 people krapnik pjkiley flbarroso yxue r2s2 grondina rpetrenko oteri oceanwind dfgreen vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros sobolevnrm Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group ibuch
	Evolutionary information for specifying a protein fold [My Copy] Nature, Vol. 437, No. 7058., pp. 512-518. by Michael Socolich, Steve W. Lockless, William P. Russ, Heather Lee, Kevin H. Gardner, Rama Ranganathan posted by 22 people dfdong ucbcjbm ana barry lna bpb Einat balajis marcius gbart analogAI nirfriedman caporaso massivemayhem structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF mingzhi bethbromley ca3295
	Guided Docking Approaches to Structure-Based Design and Screening [My Copy] Current Topics in Medicinal Chemistry, Vol. 4, No. 7. (March 2004), pp. 687-700. by X. Fradera, J. Mestres posted by 7 people Structural Biology Group TorVergata oteri LamBras dgruiz sangeetha Bioinformatics insilicodrug
	Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities. [My Copy] Biophys J, Vol. 84, No. 4. (April 2003), pp. 2273-2281. by T. M. Frimurer, G. H. Peters, L. F. Iversen, H. S. Andersen, N. P. Møller, O. H. Olsen posted by 6 people oteri dgruiz yongzhao blackbart kazemi TSRI_MGL
	SCOPPI: a structural classification of protein-protein interfaces. [My Copy] Nucleic acids research, Vol. 34, No. Database issue. (1 January 2006) by Christof Winter, Andreas Henschel, Wan Kyu K. Kim, Michael Schroeder posted by 15 people winterschlaefer higueruelo sjcockell ana kuhn bicko chad_davis marcius choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF Evangelia kintoki
	Simultaneous determination of protein structure and dynamics [My Copy] Nature, Vol. 433, No. 7022. (13 January 2005), pp. 128-132. by Kresten Lindorff-Larsen, Robert B. Best, Mark A. Depristo, Christopher M. Dobson, Michele Vendruscolo posted by 19 people Diego_Prada xdeupi Structural Biology Group TorVergata A_Coletta_Thesis karbak apaydin barry lillekatt baaden lna dgront allmensch daevans rsantana jlh64 structural_bioinformatics Bioinformatics biehl rph
	Essential dynamics of proteins [My Copy] Proteins: Structure, Function, and Genetics, Vol. 17, No. 4. (December 1993), pp. 412-425. by Andrea Amadei, Antonius B. M. Linssen, Herman J. C. Berendsen posted by 12 people kazemi Diego_Prada baaden aqeel yongzhao ttjoseph ffranca allmensch carlescorbi TSRI_MGL dimka nigham
	Side-chain flexibility in proteins upon ligand binding. [My Copy] Proteins, Vol. 39, No. 3. (15 May 2000), pp. 261-268. by R. Najmanovich, J. Kuttner, V. Sobolev, M. Edelman posted by 7 people dgruiz radestock lna yongzhao blackbart TSRI_MGL LamBras
	Rotamer Libraries in the 21st Century [My Copy] Current Opinion in Structural Biology, Vol. 12, No. 4. (1 August 2002), pp. 431-440. by R. Dunbrack posted by 12 people aqeel msuarezdiez carlosjavierna apaydin barry joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics LamBras
	Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 43. (26 October 2004), pp. 15346-15351. by B. Qian, A. R. Ortiz, D. Baker posted by 10 people aqeel ana barry lna marcius dgront structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	DrugBank: a comprehensive resource for in silico drug discovery and exploration [My Copy] Nucl. Acids Res., Vol. 34, No. suppl_1. (1 January 2006), pp. D668-672. by David S. Wishart, Craig Knox, An C. Guo, et al.Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, Jennifer Woolsey posted by 14 people sm-rush bertelsen wenhui yaredo dansullivanblk kuhn maryee sangeetha madhadron jdiggans massivemayhem Bioinformatics insilicodrug elvinado
	The relation between the divergence of sequence and structure in proteins. [My Copy] The EMBO journal, Vol. 5, No. 4. (April 1986), pp. 823-826. by C. Chothia, A. M. Lesk posted by 21 people dfdong martainn ucbcjbm bertelsen semin sgoetz cen4ik ana pansapiens jwm Einat marcius xdeupi ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
	Evolution of function in protein superfamilies, from a structural perspective [My Copy] Journal of Molecular Biology, Vol. 307, No. 4. (6 April 2001), pp. 1113-1143. by Annabel E. Todd, Christine A. Orengo, Janet M. Thornton posted by 13 people ucbcjbm flbarroso yuslinaz sgoetz ana kuhn tny sriram_s cdallett uz_labu_laimi structural_bioinformatics Bioinformatics sim82
	Side-chain flexibility in proteins upon ligand binding [My Copy] Proteins: Structure, Function, and Genetics, Vol. 39, No. 3. (2000), pp. 261-268. by Rafael Najmanovich, Josef Kuttner, Vladimir Sobolev, Marvin Edelman posted by 5 people fl yongzhao kazemi TSRI_MGL LamBras
	A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening. [My Copy] J Mol Graph Model, Vol. 18, No. 3. (June 2000) by H. B. Broughton posted by 4 people yongzhao kazemi TSRI_MGL LamBras
	Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding [My Copy] Journal of Molecular Biology, Vol. 346, No. 1. (11 February 2005), pp. 21-28. by A. Gutteridge, J. Thornton posted by 10 people nickolay boris_aguilar carlosjavierna baaden lna yongzhao alexg gbart noby TSRI_MGL
	Structural systems biology: modelling protein interactions. [My Copy] Nature reviews. Molecular cell biology, Vol. 7, No. 3. (March 2006), pp. 188-197. by Patrick Aloy, Robert B. Russell posted by 28 people flbarroso timg chica Scis0000002 ubcg08l ana aalibes bicko xico dgront drastic choonpeng henschel ruvido massivemayhem cat_worth fishtank iris_2001 gvuister lpfernandes structural_bioinformatics Bioinformatics WetBiology Evangelia andreas_foersch higueruelo chad_davis jteyra
	FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function [My Copy] Journal of Computational Chemistry, Vol. 24, No. 13. (12 August 2003), pp. 1637-1656. by Richard D. Taylor, Philip J. Jewsbury, Jonathan W. Essex posted by 5 people oteri dgruiz yongzhao blackbart TSRI_MGL
	Proteome survey reveals modularity of the yeast cell machinery [My Copy] Nature, Vol. 440, No. 7084. (22 January 2006), pp. 631-636. by Anne-Claude Gavin, Patrick Aloy, Paola Grandi, et al.Roland Krause, Markus Boesche, Martina Marzioch, Christina Rau, Lars J. Jensen, Sonja Bastuck, Birgit Dumpelfeld, Angela Edelmann, Marie-Anne Heurtier, Verena Hoffman, Christian Hoefert, Karin Klein, Manuela Hudak, Anne-Marie Michon, Malgorzata Schelder, Markus Schirle, Marita Remor, Tatjana Rudi, Sean Hooper, Andreas Bauer, Tewis Bouwmeester, Georg Casari, Gerard Drewes, Gitte Neubauer, Jens M. Rick, Bernhard Kuster, Peer Bork, Robert B. Russell, Giulio Superti-Furga posted by 42 people aceol tomhebbron ajbattle mgomes Scis0000002 lawraga bicko saket Yanno ana Borelli lfriedl ccots jmeppley chad_davis balajis xico shantanu nirfriedman balabu dgront noano koller ruvido nicoleq lpfernandes structural_bioinformatics kdl MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology WetBiology phoenixzxl larsjuhljensen ellakat frohike carlk ethkim
	Modelling protein docking using shape complementarity, electrostatics and biochemical information [My Copy] Journal of Molecular Biology, Vol. 272, No. 1. (12 September 1997), pp. 106-120. by Henry A. Gabb, Richard M. Jackson, Michael J. Sternberg posted by 12 people apaydin jwm bicko yongzhao ima ffranca cjeans selrac Radiation_Damage Stressosome TSRI_MGL kintoki
	Allosteric determinants in guanine nucleotide-binding proteins. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 14445-14450. by M. E. Hatley, S. W. Lockless, S. K. Gibson, A. G. Gilman, R. Ranganathan posted by 11 people qluo barry lna Einat marcius caporaso structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
	Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 1. (2006), pp. 164-179. by Amarda Shehu, Cecilia Clementi, Lydia E. Kavraki posted by 9 people apaydin nigham aqeel yongzhao elham hmk sobolevnrm TSRI_MGL baker-group
	Fragnostic: walking through protein structure space. [My Copy] Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005) by I. Friedberg, A. Godzik posted by 12 people ana barry pansapiens aalibes Einat marcius alexg eweaver structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Natural-like function in artificial WW domains [My Copy] Nature, Vol. 437, No. 7058., pp. 579-583. by William P. Russ, Drew M. Lowery, Prashant Mishra, Michael B. Yaffe, Rama Ranganathan posted by 12 people ana barry balajis marcius caporaso structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF bethbromley ca3295
	Local complexity of amino acid interactions in a protein core. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 1. (6 January 2004), pp. 111-116. by R. K. Jain, R. Ranganathan posted by 10 people ana barry lna marcius gbart choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Fragment-based drug discovery. [My Copy] J Med Chem, Vol. 47, No. 14. (1 July 2004), pp. 3463-3482. by D. A. Erlanson, R. S. McDowell, T. O'Brien posted by 6 people Fragment Based Drug Discovery pslee nachtalp sangeetha Bioinformatics insilicodrug
	A pharmacophore docking algorithm and its application to the cross-docking of 18 HIV-NNRTI's in their binding pockets. [My Copy] Proteins, Vol. 54, No. 3. (15 February 2004), pp. 526-533. by F. Daeyaert, M. de Jonge, J. Heeres, et al.L. Koymans, P. Lewi, M. H. Vinkers, P. A. Janssen posted by 3 people nachtalp yongzhao TSRI_MGL
	An efficient molecular docking using conformational space annealing. [My Copy] J Comput Chem, Vol. 26, No. 1. (15 January 2005), pp. 78-87. by K. Lee, C. Czaplewski, S. Y. Kim, J. Lee posted by 3 people nachtalp yongzhao TSRI_MGL
	Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock [My Copy] Proteins: Structure, Function, and Genetics, Vol. 46, No. 1. (15 November 2001), pp. 34-40. by Fredrik österberg, Garrett M. Morris, Michel F. Sanner, Arthur J. Olson, David S. Goodsell posted by 5 people Structural Biology Group TorVergata oteri yongzhao peprovy TSRI_MGL
	Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibility [My Copy] Journal of Computational Chemistry, Vol. 23, No. 16. (2002), pp. 1656-1670. by Visvaldas Kairys, Michael K. Gilson posted by 6 people yongzhao blackbart kazemi TSRI_MGL arlam Chang group
	Development and evaluation of a generic evolutionary method for protein-ligand docking [My Copy] Journal of Computational Chemistry, Vol. 25, No. 6. (27 February 2004), pp. 843-857. by Jinn-Moon Yang posted by 4 people dgruiz nachtalp yongzhao TSRI_MGL
	Current status of virtual screening as analysed by target class. [My Copy] Med Chem, Vol. 2, No. 1. (January 2006), pp. 89-112. by M. J. Stoermer posted by 5 people yongzhao marcius TSRI_MGL BioinfoCIPF SGU-CIPF
	Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 10. (13 May 2003), pp. 5772-5777. by B. Ma, T. Elkayam, H. Wolfson, R. Nussinov posted by 13 people tbinbal dkoveal mdimmic barry bicko lyongu nickolay choonpeng cjeans carlescorbi structural_bioinformatics Bioinformatics ladab
	A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. [My Copy] J Med Chem, Vol. 45, No. 8. (11 April 2002), pp. 1712-1722. by S. L. McGovern, E. Caselli, N. Grigorieff, B. K. Shoichet posted by 5 people LamBras lna sangeetha Bioinformatics insilicodrug
	Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. [My Copy] Angewandte Chemie (International ed. in English), Vol. 42, No. 24. (23 June 2003), pp. 2718-2736. by Andrew M. Davis, Simon J. Teague, Gerard J. Kleywegt posted by 6 people oteri apaydin sangeetha Bioinformatics insilicodrug thanatos
	Modelling and simulation: a computational perspective in anticancer drug discovery. [My Copy] Curr Med Chem Anticancer Agents, Vol. 4, No. 5. (September 2004), pp. 401-403. by F. Gago posted by 6 people marcius sangeetha Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
	New methodologies for ligand-based virtual screening. [My Copy] Curr Pharm Des, Vol. 11, No. 9. (2005), pp. 1189-1202. by F. L. Stahura, J. Bajorath posted by 6 people marcius sangeetha Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
	Protein docking using a genetic algorithm [My Copy] Proteins: Structure, Function, and Genetics, Vol. 44, No. 1. (8 May 2001), pp. 44-56. by Eleanor J. Gardiner, Peter Willett, Peter J. Artymiuk posted by 7 people dgruiz rmj001 bicko yongzhao cjeans TSRI_MGL timgeppert
	An analysis of core deformations in protein superfamilies. [My Copy] Biophys J, Vol. 88, No. 2. (February 2005), pp. 1291-1299. by A. Leo-Macias, P. Lopez-Romero, D. Lupyan, D. Zerbino, A. R. Ortiz posted by 10 people apaydin ana barry lna dimka aqeel insectopalo structural_bioinformatics Bioinformatics edvin
	Conformer generation under restraints. [My Copy] Curr Opin Struct Biol, Vol. 16, No. 2. (April 2006), pp. 160-165. by P. I. de Bakker, N. Furnham, T. L. Blundell, M. A. DePristo posted by 5 people aqeel yongzhao dgront rabio TSRI_MGL
	Efficient docking of peptides to proteins without prior knowledge of the binding site. [My Copy] Protein science : a publication of the Protein Society. , Vol. 11, No. 7. (July 2002), pp. 1729-1737. by Csaba Hetényi, David van der Spoel posted by 6 people npt11tpn Structural Biology Group TorVergata oteri yongzhao TSRI_MGL rguenther
	NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps [My Copy] Acta Crystallographica Section D: Biological Crystallography, Vol. 62, No. 9. (01 September 2006), pp. 1098-1100. by Suhre, K., Navaza, J., Sanejouand, -H posted by 6 people martainn dawnsong apaydin aqeel yongzhao TSRI_MGL
	Accounting for global protein deformability during protein-protein and protein-ligand docking. [My Copy] Biochim Biophys Acta (5 October 2005) by Andreas May, Martin Zacharias posted by 5 people flbarroso yongzhao alexg qzhang TSRI_MGL
	Hierarchical docking of databases of multiple ligand conformations. [My Copy] Curr Top Med Chem, Vol. 5, No. 8. (2005), pp. 739-749. by D. M. Lorber, B. K. Shoichet posted by 4 people oteri yongzhao blackbart TSRI_MGL
	Ligand binding affinities from MD simulations. [My Copy] Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 358-365. by J. Aqvist, V. B. Luzhkov, B. O. Brandsdal posted by 7 people flbarroso barry baaden dimka superpyrin structural_bioinformatics Bioinformatics
	Do structurally similar molecules have similar biological activity? [My Copy] J Med Chem, Vol. 45, No. 19. (12 September 2002), pp. 4350-4358. by Y. C. Martin, J. L. Kofron, L. M. Traphagen posted by 5 people reyez kuhn sangeetha Bioinformatics insilicodrug
	Structure validation by Calpha geometry: phi,psi and Cbeta deviation [My Copy] Proteins, Vol. 50, No. 3. (15 February 2003), pp. 437-450. by Simon C. Lovell, Ian W. Davis, Arendall, et al.Paul I. de Bakker, Michael J. Word, Michael G. Prisant, Jane S. Richardson, David C. Richardson posted by 10 people mikelape barry sangeetha joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
	'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments [My Copy] Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 129-133. by Jean-Christophe Gelly, Alexandre G. de Brevern, Serge Hazout posted by 11 people ana barry dimka ttjoseph marcius nickolay choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Protein flexibility predictions using graph theory [My Copy] Proteins: Structure, Function, and Genetics, Vol. 44, No. 2. (29 May 2001), pp. 150-165. by Donald J. Jacobs, A. J. Rader, Leslie A. Kuhn, M. F. Thorpe posted by 9 people Scis0000002 fl ana aqeel peprovy smenor structural_bioinformatics Bioinformatics LamBras
	Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. [My Copy] J Mol Biol, Vol. 291, No. 1. (6 August 1999), pp. 177-196. by L. A. Mirny, E. I. Shakhnovich posted by 9 people dfdong ana barry Einat marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Protein flexibility and drug design: how to hit a moving target [My Copy] Current Opinion in Chemical Biology, Vol. 6, No. 4. (1 August 2002), pp. 447-452. by Heather A. Carlson posted by 3 people yongzhao TSRI_MGL LamBras
	Trends in Virtual Combinatorial Library Design [My Copy] pp. 2095-2101. by G. Schneider posted by 3 people LamBras yongzhao TSRI_MGL
	M-score: a knowledge-based potential scoring function accounting for protein atom mobility. [My Copy] J Med Chem, Vol. 49, No. 20. (5 October 2006), pp. 5903-5911. by C. Y. Yang, R. Wang, S. Wang posted by 4 people mijam yongzhao kazemi TSRI_MGL
	The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. [My Copy] Biopolymers, Vol. 68, No. 1. (January 2003), pp. 47-62. by J. H. Lin, A. L. Perryman, J. R. Schames, J. A. McCammon posted by 9 people karinaecomp barry blackbart kazemi sobolevnrm structural_bioinformatics Bioinformatics baker-group LamBras
	Understanding nature's catalytic toolkit. [My Copy] Trends Biochem Sci (5 October 2005) by Alex Gutteridge, Janet M M. Thornton posted by 16 people ucbcjbm ana jwm Einat alexg gbart eweaver tny noby siebertm structural_bioinformatics Radiation_Damage Stressosome Bioinformatics grottenolm sim82
	Conformational changes studied by cryo-electron microscopy. [My Copy] Nat Struct Biol, Vol. 7, No. 9. (September 2000), pp. 711-714. by H. R. Saibil posted by 4 people aqeel yongzhao dgront TSRI_MGL
	Practical lessons from protein structure prediction. [My Copy] Nucleic Acids Res, Vol. 33, No. 6. (2005), pp. 1874-1891. by K. Ginalski, N. V. Grishin, A. Godzik, L. Rychlewski posted by 13 people mcbla ana aalibes thaliana okarsligil marcius duartemolha dgront mirzazadeh structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Small molecule antagonists of proteins. [My Copy] Biochem Pharmacol, Vol. 65, No. 1. (1 January 2003), pp. 1-8. by T. R. Gadek, J. B. Nicholas posted by 5 people dgruiz sangeetha Bioinformatics insilicodrug higueruelo
	Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. [My Copy] J Med Chem, Vol. 47, No. 2. (15 January 2004), pp. 337-344. by Z. Deng, C. Chuaqui, J. Singh posted by 7 people bio_dataminer ubcg08l apostola sangeetha Bioinformatics insilicodrug massivemayhem
	CATH--a hierarchic classification of protein domain structures. [My Copy] Structure (London, England : 1993), Vol. 5, No. 8. (15 August 1997), pp. 1093-1108. by C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, J. M. Thornton posted by 19 people ucbcjbm flbarroso kumar_physics semin sebk tjimenez dimka jwm chad_davis Einat caporaso structural_bioinformatics Radiation_Damage Stressosome biomedical-nlp massivemayhem sim82 jteyra gulkur
	Novel technologies for virtual screening. [My Copy] Drug Discov Today, Vol. 9, No. 1. (1 January 2004), pp. 27-34. by T. Lengauer, C. Lemmen, M. Rarey, M. Zimmermann posted by 6 people zimbo1 tjimenez sangeetha ramensky Bioinformatics insilicodrug
	Localization of protein-binding sites within families of proteins. [My Copy] Protein Sci, Vol. 14, No. 9. (September 2005), pp. 2350-2360. by D. Korkin, F. P. Davis, A. Sali posted by 9 people barry tjimenez bicko marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF wilbur
	Interrogating protein interaction networks through structural biology. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 9. (30 April 2002), pp. 5896-5901. by P. Aloy, R. B. Russell posted by 17 people kgutwin tomhebbron bpcusack ana barry baaden bicko lfriedl chad_davis henschel ruvido cjeans tale structural_bioinformatics kdl Bioinformatics Evangelia
	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. [My Copy] Nucleic acids research, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402. by S. F. Altschul, T. L. Madden, A. A. Schäffer, et al.J. Zhang, Z. Zhang, W. Miller, D. J. Lipman posted by 74 people rshe niallhaslam ucbcjbm timhubbard parnell tfuji maria_hauser jbhiatt yylin mgomes BioNica idoerg pjcite swp09 kgutwin mcbla cpwardell References for 3DSim paper johanviklund daforerog nlapalu sebk tjimenez shung pwais dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 EisenLab biomedical-nlp Microbial-Ecology Plantandetc mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM
	GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447. by Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl posted by 26 people sunnytov softsimu parnell rabio oteri krapnik robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi Structural Biology Group TorVergata A_Coletta_Thesis choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm baker-group r2s2 middledomain loison
	Clustering of low-energy conformations near the native structures of small proteins. [My Copy] Proc Natl Acad Sci U S A, Vol. 95, No. 19. (15 September 1998), pp. 11158-11162. by D. Shortle, K. T. Simons, D. Baker posted by 9 people barry thaliana dgront joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	Efficient method for high-throughput virtual screening based on flexible docking: discovery of novel acetylcholinesterase inhibitors. [My Copy] J Med Chem, Vol. 47, No. 20. (23 September 2004), pp. 4818-4828. by M. Y. Mizutani, A. Itai posted by 7 people sangeetha joergkurtwegner Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
	Protein flexibility prediction by an all-atom mean-field statistical theory. [My Copy] Protein Sci, Vol. 14, No. 7. (July 2005), pp. 1772-1777. by B. P. Pandey, C. Zhang, X. Yuan, J. Zi, Y. Zhou posted by 6 people baaden aqeel yongzhao jessicaopacic TSRI_MGL LabCompMed
	New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy [My Copy] Journal of Computational Chemistry, Vol. 26, No. 11. (2005), pp. 1089-1095. by A. M. Ruvinsky, A. V. Kozintsev posted by 3 people yongzhao daevans TSRI_MGL
	Exploring Global Motions and Correlations in the Ribosome. [My Copy] Biophys J (10 June 2005) by Joanna Trylska, Valentina Tozzini, J Andrew A. McCammon posted by 7 people apaydin baaden anita yongzhao eckart_bindewald structure-bii TSRI_MGL
	A new progressive-iterative algorithm for multiple structure alignment. [My Copy] Bioinformatics (7 June 2005) by Dmitry Lupyan, Alejandra Leo-Macias, Angel R R. Ortiz posted by 10 people tomjad sebk ana dimka marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF tjimenez
	Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 6. (1 November 2007), pp. 2312-2334. by Jianyin Shao, Stephen W. Tanner, Nephi Thompson, Thomas E. Cheatham posted by 14 people karinaecomp anuragsethi Diego_Prada scampos Structural Biology Group TorVergata oteri barry daevans sobolevnrm structural_bioinformatics baker-group LamBras allmensch GermanErlenkamp
	Cyclic coordinate descent: A robotics algorithm for protein loop closure. [My Copy] Protein Sci, Vol. 12, No. 5. (May 2003), pp. 963-972. by A. A. Canutescu, R. L. Dunbrack posted by 6 people vavi yongzhao j3xucite dgront TSRI_MGL mijam
	Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. [My Copy] J Mol Biol, Vol. 344, No. 3. (26 November 2004), pp. 781-795. by X. Li, O. Keskin, B. Ma, R. Nussinov, J. Liang posted by 13 people barry baaden bicko nickolay j3xucite bluvsh1 xz grahamc structural_bioinformatics Bioinformatics Evangelia ladab paolomarcatili
	Flexible docking in solution using metadynamics. [My Copy] J Am Chem Soc, Vol. 127, No. 8. (2 March 2005), pp. 2600-2607. by F. L. Gervasio, A. Laio, M. Parrinello posted by 5 people A_Coletta_Thesis apaydin baaden yongzhao TSRI_MGL