LamBras's Top Recommendations

These recommendations were last updated about 2 hours ago.

	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
	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
	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
	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
	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
	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
	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
	Protein-ligand docking: Current status and future challenges. [My Copy] Proteins (21 July 2006) by Sérgio Filipe F. Sousa, Pedro Alexandrino A. Fernandes, Maria João J. Ramos posted by 13 people flbarroso ramensky BragilMassoud yongzhao peprovy kazemi sergio_fms carlescorbi TSRI_MGL robert boris_aguilar qaiser_fatmi Chang group
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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 25 people 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
	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
	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
	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
	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
	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
	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
	The MARTINI Coarse-Grained Force Field: Extension to Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 5. (1 May 2008), pp. 819-834. by Luca Monticelli, Senthil K. Kandasamy, Xavier Periole, Ronald G. Larson, D. Peter Tieleman, Siewert-Jan Marrink posted by 17 people arnaucordomi dimka oteri sunrise flbarroso Structural Biology Group TorVergata A_Coletta_Thesis krapnik Molecular dynamics in MSU Marine middledomain sobolevnrm baker-group Ema aqeel DanielParton softsimu
	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
	Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms1 [My Copy] Journal of Molecular Biology, Vol. 285, No. 4. (29 January 1999), pp. 1711-1733. by Word, Simon C. Lovell, Thomas H. Labean, et al.Hope C. Taylor, Michael E. Zalis, Brent K. Presley, Jane S. Richardson, David C. Richardson posted by 10 people Diego_Prada aqeel dgront barry joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	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
	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
	Dynamic personalities of proteins [My Copy] Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972. by Katherine Henzler-Wildman, Dorothee Kern posted by 20 people saravan Diego_Prada xdeupi viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans sobolevnrm baker-group wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor
	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
	Comparison of multiple Amber force fields and development of improved protein backbone parameters. [My Copy] Proteins, Vol. 65, No. 3. (15 November 2006), pp. 712-725. by Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling posted by 11 people arnaucordomi Vadikus bmduggan baaden lna allmensch choonpeng kazemi barry GermanErlenkamp RamuAnandakrishnan
	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
	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
	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
	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 25 people 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
	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
	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
	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
	Flexibility and packing in proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 3. (5 February 2002), pp. 1274-1279. by Bertil Halle posted by 11 people Diego_Prada edws barry baker-group sobolevnrm ana aqeel allmensch hmk 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
	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
	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 21 people ucbcjbm ana barry lna bpb Einat balajis marcius gbart analogAI nirfriedman caporaso massivemayhem structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF mingzhi bethbromley ca3295
	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
	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
	ROCR: visualizing classifier performance in R. [My Copy] Bioinformatics (11 August 2005) by Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer posted by 16 people natstreet druvus BragilMassoud ana barry Ayest lyongu marcius schlauchi gokhan za structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF bertelsen
	Calculation of protein-ligand binding affinities. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 36 (2007), pp. 21-42. by Michael K. Gilson, Huan-Xiang X. Zhou posted by 19 people mijogiffin Chang group flbarroso GermanErlenkamp onufriev arlam Structural Biology Group TorVergata oteri McCammon jmccammon bmduggan dimka neils hmk ashaytan ras cchang boris_aguilar qaiser_fatmi
	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
	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
	Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach. [My Copy] Proteins, Vol. 56, No. 2. (1 August 2004), pp. 322-337. by H. Gohlke, L. A. Kuhn, D. A. Case posted by 7 people bmduggan barry lna aqeel blackbart structural_bioinformatics 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
	Protein-protein binding is often associated with changes in protonation state [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Aaron C. Mason, Jan H. Jensen posted by 10 people flbarroso onufriev csrocha bicko sobolevnrm baker-group RamuAnandakrishnan barry structural_bioinformatics McCammon
	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
	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
	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
	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
	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
	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
	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
	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
	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
	Recent advances in implicit solvent-based methods for biomolecular simulations. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (04 April 2008), pp. 140-148. by Jianhan Chen, Charles L. Brooks, Jana Khandogin posted by 10 people RamuAnandakrishnan mikaellund Structural Biology Group TorVergata oteri nickolay flbarroso choonpeng sobolevnrm baker-group onufriev
	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
	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
	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
	Flexible ligand docking to multiple receptor conformations: a practical alternative. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (April 2008), pp. 178-184. by M. Totrov, R. Abagyan posted by 7 people klexa oteri structural_bioinformatics McCammon Bioinformatics barry aqeel
	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
	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
	Flexibility and conformational entropy in protein-protein binding. [My Copy] Structure, Vol. 14, No. 4. (April 2006), pp. 683-693. by R. Grünberg, M. Nilges, J. Leckner posted by 9 people hmk raik barry pansapiens lna aqeel allmensch structural_bioinformatics Bioinformatics
	What is principal component analysis? [My Copy] Nature Biotechnology, Vol. 26, No. 3. (01 March 2008), pp. 303-304. by Markus Ringner posted by 73 people singhsh Jporci tnhh ruvido ucbcjbm daforerog Diego_Prada abellogin nguizard thegoose2 arsyed Zephyrus flips svozil VGreiff kaniko ssgong Yanno guhjy operon barry baaic dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu rsantana sobolevnrm baker-group fryanpan kengg rvosa FAB-lab dekay23 adacier Bioinformatics hpaces waghsk rchauhan pavanghatty kristgy jfr bibay2004 xingxu quianominorleo craigwilson06 ashko markusd dayjm dimka i-stevenson chrissp100 tharris ale mjoach HugoMarcelo jdiezperezj rrbarb Nici
	Protein-protein interactions: a review of protein dimer structures. [My Copy] Prog Biophys Mol Biol, Vol. 63, No. 1. (1995), pp. 31-65. by S. Jones, J. M. Thornton posted by 10 people viktor21614 bicko barry chad_davis joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	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
	Transition networks for modeling the kinetics of conformational change in macromolecules [My Copy] Current Opinion in Structural Biology In Theory and simulation / Macromolecular assemblages, Vol. 18, No. 2. (April 2008), pp. 154-162. by Frank Noé, Stefan Fischer posted by 9 people Diego_Prada aqeel barry sobolevnrm structural_bioinformatics baker-group paulschlesinger McCammon toerst
	sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank. [My Copy] J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 717-727. by E. Kellenberger, P. Muller, C. Schalon, G. Bret, N. Foata, D. Rognan posted by 8 people BragilMassoud caporaso schlauchi daevans ramensky biomedical-nlp sim82 nickolay
	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
	Predicting Absolute Ligand Binding Free Energies to a Simple Model Site [My Copy] Journal of Molecular Biology, Vol. 371, No. 4. (24 August 2007), pp. 1118-1134. by David L. Mobley, Alan P. Graves, John D. Chodera, Andrea C. Mcreynolds, Brian K. Shoichet, Ken A. Dill posted by 10 people allmensch oteri barry insilico daevans superpyrin structural_bioinformatics Bioinformatics dmobley Computer Aided Drug Design
	The packing density in proteins: standard radii and volumes1 [My Copy] Journal of Molecular Biology, Vol. 290, No. 1. (02 July 1999), pp. 253-266. by Jerry Tsai, Robin Taylor, Cyrus Chothia, Mark Gerstein posted by 10 people sebk ana barry bicko blackbart medic0747 structural_bioinformatics Bioinformatics sobolevnrm baker-group
	Identifying protein folding cores from the evolution of flexible regions during unfolding. [My Copy] J Mol Graph Model, Vol. 21, No. 3. (December 2002), pp. 195-207. by B. M. Hespenheide, A. J. Rader, M. F. Thorpe, L. A. Kuhn posted by 6 people apaydin lna aqeel blackbart choonpeng higueruelo
	Application of a Theory of Enzyme Specificity to Protein Synthesis [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 44, No. 2. (February 1958), pp. 98-104. by D. E. Koshland posted by 8 people aqeel cen4ik apostola robert kazemi nigham sim82 boris_aguilar
	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
	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
	Intrinsic motions along an enzymatic reaction trajectory. [My Copy] Nature, Vol. 450, No. 7171. (6 December 2007), pp. 838-844. by Katherine A. Henzler-Wildman, Vu Thai, Ming Lei, et al.Maria Ott, Magnus Wolf-Watz, Tim Fenn, Ed Pozharski, Mark A. Wilson, Gregory A. Petsko, Martin Karplus, Christian G. Hübner, Dorothee Kern posted by 14 people saravan ahmetbakan xdeupi ubcg08l ruvido barry aqeel ebeutler cactus sobolevnrm paulschlesinger jlh64 baker-group yalexeev
	Calculation of protein-ligand binding free energy by using a polarizable potential [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295. by Dian Jiao, Pavel A. Golubkov, Thomas A. Darden, Pengyu Ren posted by 9 people flbarroso onufriev jmccammon biehl sobolevnrm baker-group barry structural_bioinformatics McCammon
	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
	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
	A method for biomolecular structural recognition and docking allowing conformational flexibility. [My Copy] J Comput Biol, Vol. 5, No. 4. (1998), pp. 631-654. by B. Sandak, R. Nussinov, H. J. Wolfson posted by 3 people yongzhao kazemi TSRI_MGL
	A Critical Assessment of Docking Programs and Scoring Functions [My Copy] J. Med. Chem., Vol. 49, No. 20. (5 October 2006), pp. 5912-5931. by G. L. Warren, C. W. Andrews, A. M. Capelli, et al.B. Clarke, J. Lalonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, M. S. Head posted by 7 people skoddet ucbcjbm BragilMassoud aalibes schlauchi daevans superpyrin
	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
	Recent Advances in Docking and Scoring [My Copy] Current Computer - Aided Drug Design, Vol. 1, No. 1. (January 2005), pp. 93-102. by E. M. Krovat, T. Steindl, T. Langer posted by 4 people yongzhao kazemi TSRI_MGL pmalatino
	REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes [My Copy] Biophys. J. (9 May 2008), biophysj.108.131714. by Kei Moritsugu, Jeremy C. Smith posted by 10 people barry baker-group sobolevnrm A_Coletta_Thesis paulschlesinger choonpeng aqeel jmccammon McCammon rok
	Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (12 August 2008), pp. 11182-11187. by Kei-ichi Okazaki, Shoji Takada posted by 11 people oteri bmduggan xdeupi okapi aqeel raik ruvido structural_bioinformatics McCammon barry zwang
	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
	A geometric approach to macromolecule-ligand interactions. [My Copy] J Mol Biol, Vol. 161, No. 2. (25 October 1982), pp. 269-288. by I. D. Kuntz, J. M. Blaney, S. J. Oatley, R. Langridge, T. E. Ferrin posted by 4 people Diego_Prada dfgreen BragilMassoud kazemi
	Bridging from molecular simulation to biochemical networks. [My Copy] Curr Opin Struct Biol, Vol. 17, No. 2. (April 2007), pp. 166-172. by M. Stein, R. R. Gabdoulline, R. C. Wade posted by 11 people anuragsethi choonpeng Structural Biology Group TorVergata oteri ocs aqeel Borelli cmmorel julius ras higueruelo
	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
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry, Vol. 30, No. 6. (2009), pp. 864-872. by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, et al.Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande posted by 14 people anuragsethi kevinchannon flbarroso r2s2 iantunbridge ihaque baker-group sobolevnrm ruvido massivemayhem structural_bioinformatics McCammon barry RamuAnandakrishnan