Tag protein_ligand [57 articles] Export Sort

Recent papers classified by the tag protein_ligand.

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	Inclusion of ionization states of ligands in affinity calculations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 1. (2009), pp. 138-150. by Serena Donnini, Alessandra Villa, Gerrit Groenhof, Alan E. Mark, Rik K. Wierenga, André H. Juffer posted to protein_ligand pka by onufriev on 2009-11-04 23:52:27 as along with 5 people and 2 groups flbarroso rbaron ibuch sobolevnrm RamuAnandakrishnan McCammon baker-group
	Chemical biology: Caught in the activation [My Copy] Nature, Vol. 461, No. 7263. (23 September 2009), pp. 484-485. by Yi Liu posted to structure protein_ligand drug_design by boris_aguilar on 2009-09-24 06:35:30 as along with 1 person alexknight
	Structural identification of the pathway of long-range communication in an allosteric enzyme [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 6. (12 February 2008), pp. 1832-1837. by Prafull S. Gandhi, Zhiwei Chen, F. Scott Mathews, Enrico Di Cera posted to protein_mechanics protein_ligand general_interest by boris_aguilar on 2009-09-11 23:59:31 as along with 3 people and 1 group lna cactus sobolevnrm baker-group
	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 to protein_mechanics protein_ligand pka by boris_aguilar on 2009-09-09 18:09:27 as along with 9 people and 1 group richardbickerton apaydin skywalkerus02 sobolevnrm klexa oteri bmduggan barry zwang McCammon
	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 to protein_ligand pka by onufriev on 2009-08-26 02:25:09 as along with 8 people and 6 groups chemrahul82 pablocarb bicko barry sangeetha blackbart joergkurtwegner skoddet structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
	A simple physical model for binding energy hot spots in proteinâprotein complexes [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121. by Tanja Kortemme, David Baker posted to protein_ligand by onufriev on 2009-08-26 02:22:57 as along with 8 people and 1 group chemrahul82 oceanwind lna jwm bicko cjeans hmk skoddet Nielsen group
	The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14349-14354. by Ahmet Bakan, Ivet Bahar posted to protein_mechanics protein_ligand drug_design by boris_aguilar on 2009-08-23 02:09:18 as along with 6 people and 1 group mittinatten ahmetbakan apaydin anuragsethi jmccammon okapi McCammon
	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 to docking protein_ligand structure by boris_aguilar on 2009-08-04 02:23:49 as along with 8 people and 1 group nickolay carlosjavierna baaden lna yongzhao alexg gbart noby TSRI_MGL
	An analysis of conformational changes on proteinprotein association: implications for predictive docking [My Copy] Protein Eng., Vol. 12, No. 4. (1 April 1999), pp. 271-283. by Matthew J. Betts, Michael J. E. Sternberg posted to docking protein_ligand structure by boris_aguilar on 2009-08-03 21:19:26 as along with 4 people mijogiffin bicko ffranca chad_davis
	Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies [My Copy] Journal of the American Chemical Society, Vol. 121, No. 36. (1 September 1999), pp. 8133-8143. by Irina Massova, Peter A. Kollman posted to protein_ligand by onufriev on 2009-07-18 07:58:40 as along with 2 people chemrahul82 boris_aguilar
	Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. [My Copy] J Mol Biol, Vol. 330, No. 4. (18 July 2003), pp. 891-913. by H. Gohlke, C. Kiel, D. A. Case posted to protein_ligand by onufriev on 2009-05-21 08:15:07 as along with 2 people bmduggan lillekatt
	Dynamic Dysfunction in Dihydrofolate Reductase Results from Antifolate Drug Binding: Modulation of Dynamics within a Structural State [My Copy] Structure, Vol. 17, No. 3. (11 March 2009), pp. 386-394. by Randall V. Mauldin, Mary J. Carroll, Andrew L. Lee posted to allosteric nmr protein_ligand by barry to the group structural_bioinformatics on 2009-04-23 03:06:51 as along with 1 person and 1 group ae1054 McCammon
	Trapping Moving Targets with Small Molecules [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 213-215. by Gregory M. Lee, Charles S. Craik posted to protein_ligand review by barry to the group structural_bioinformatics on 2009-04-23 02:48:45 as along with 6 people and 2 groups guhjy nanonan sobolevnrm pablocarb Fortran friendpine baker-group McCammon
	2D molecular graphics: a flattened world of chemistry and biology [My Copy] Brief Bioinform (30 March 2009), bbp013. by Peng Zhou, Zhicai Shang posted to protein_ligand by barry to the group structural_bioinformatics on 2009-04-23 02:21:12 as along with 5 people and 2 groups mijogiffin Zephyrus nanonan sobolevnrm dimka baker-group McCammon
	Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites [My Copy] BMC Structural Biology, Vol. 8 (27 October 2008), 45. by Andrew T. Binkowski, Andrzej Joachimiak posted to protein_ligand structure_comparison by barry to the group structural_bioinformatics on 2009-03-25 22:12:20 as along with 2 people and 2 groups GeeSharpMinor sobolevnrm Bioinformatics baker-group
	Predicting Protein Function and Binding Profile via Matching of Local Evolutionary and Geometric Surface Patterns [My Copy] Journal of Molecular Biology, Vol. 387, No. 2. (27 March 2009), pp. 451-464. by Yan Y. Tseng, Joseph Dundas, Jie Liang posted to protein_ligand protein_structure by barry to the group structural_bioinformatics on 2009-03-24 19:01:32 as along with 3 people and 3 groups sobolevnrm pablocarb nickolay McCammon Bioinformatics baker-group
	Observation of a Short, Strong Hydrogen Bond in the Active Site of Hydroxynitrile Lyase from Hevea brasiliensis Explains a Large pKa Shift of the Catalytic Base Induced by the Reaction Intermediate [My Copy] J. Biol. Chem., Vol. 279, No. 5. (30 January 2004), pp. 3699-3707. by Gudrun R. Stranzl, Karl Gruber, Georg Steinkellner, Klaus Zangger, Helmut Schwab, Christoph Kratky posted to drug_design pka protein_ligand by boris_aguilar on 2009-02-12 01:59:01 as
	Dissecting the Electrostatic Interactions and pH-Dependent Activity of a Family 11 Glycosidase†,‡ [My Copy] Biochemistry, Vol. 40, No. 34. (2001), pp. 10115-10139. by Manish D. Joshi, Gary Sidhu, Jens E. Nielsen, Gary D. Brayer, Stephen G. Withers, Lawrence P. Mcintosh posted to drug_design pka protein_ligand by boris_aguilar on 2009-02-12 01:54:23 as
	A New Concept for the Mechanism of Action of Chymotrypsin: The Role of the Low-Barrier Hydrogen Bond† [My Copy] Biochemistry, Vol. 36, No. 15. (1 April 1997), pp. 4576-4584. by Constance S. Cassidy, Jing Lin, Perry A. Frey posted to drug_design pka protein_ligand by boris_aguilar on 2009-02-12 01:47:14 as
	NMR and X-ray Evidence That the HIV Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor [My Copy] Journal of the American Chemical Society, Vol. 116, No. 23. (1 November 1994), pp. 10791-10792. by Toshimasa Yamazaki, Linda K. Nicholson, Paul Wingfield, et al.Stephen J. Stahl, Joshua D. Kaufman, Charles J. Eyermann, Nicholas C. Hodge, Patrick Y. Lam, D. A. Torchia, posted to drug_design pka protein_ligand by boris_aguilar on 2009-02-12 01:41:22 as
	Dissection of the pH Dependence of Inhibitor Binding Energetics for an Aspartic Protease: Direct Measurement of the Protonation States of the Catalytic Aspartic Acid Residues†,‡ [My Copy] Biochemistry, Vol. 36, No. 51. (1 December 1997), pp. 16166-16172. by Dong Xie, Sergei Gulnik, Laura Collins, Elena Gustchina, Leonid Suvorov, John W. Erickson posted to drug_design pka protein_ligand by boris_aguilar on 2009-02-12 01:33:20 as
	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 to protein_ligand by onufriev on 2009-02-04 20:47:08 as along with 15 people and 3 groups mijogiffin flbarroso GermanErlenkamp arlam oteri jmccammon bmduggan dimka neils hmk ashaytan ras cchang boris_aguilar qaiser_fatmi Chang group Structural Biology Group TorVergata McCammon
	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 to protein_ligand by onufriev on 2009-01-31 23:12:25 as along with 6 people and 3 groups krapnik flbarroso jmccammon biehl sobolevnrm barry baker-group structural_bioinformatics McCammon
	Calculation of absolute protein-ligand binding free energy using distributed replica sampling. [My Copy] The Journal of chemical physics, Vol. 129, No. 15. (21 October 2008) by T. Rodinger, P. L. Howell, R. Pomès posted to protein_ligand by onufriev on 2009-01-31 23:05:38 as along with 2 people flbarroso kentsis
	Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems [My Copy] Journal of Computational Chemistry, Vol. 26, No. 7. (2005), pp. 668-681. by Peter A. Sims, Chung F. Wong, Danka Vuga, Andrew J. Mccammon, Bartholomew M. Sefton posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-28 00:16:53 as
	Charge optimization of the interface between protein kinases and their ligands. [My Copy] Journal of computational chemistry, Vol. 25, No. 11. (August 2004), pp. 1416-1429. by P. A. Sims, C. F. Wong, J. A. McCammon posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-28 00:14:26 as along with 1 person dfgreen
	Mutational analysis and protein engineering of receptor-binding determinants in human placental lactogen [My Copy] J. Biol. Chem., Vol. 266, No. 17. (15 June 1991), pp. 10982-10988. by H. B. Lowman, B. C. Cunningham, J. A. Wells posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-28 00:10:32 as
	Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface. [My Copy] Proteins, Vol. 60, No. 4. (1 September 2005), pp. 644-657. by D. F. Green, B. Tidor posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-28 00:04:34 as along with 1 person dfgreen
	Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide [My Copy] Nature, Vol. 425, No. 6956. (25 September 2003), pp. 423-427. by Kenneth C. Holmes, Isabel Angert, F. Jon Kull, Werner Jahn, Rasmus R. Schroder posted to docking pka protein_ligand by boris_aguilar on 2009-01-26 17:58:39 as along with 1 person ckmyo
	Conformational changes associated with protein-protein interactions [My Copy] Current Opinion in Structural Biology, Vol. 14, No. 1. (February 2004), pp. 104-109. by Chern-Sing Goh, Duncan Milburn, Mark Gerstein posted to docking pka protein_ligand by boris_aguilar on 2009-01-26 17:56:07 as along with 5 people flbarroso LamBras apaydin bicko nigham
	Organization and functions of interacting domains for signaling by protein-protein interactions. [My Copy] Sci STKE, Vol. 2003, No. 209. (18 November 2003) by E. Buck, R. Iyengar posted to docking pka protein_ligand by boris_aguilar on 2009-01-26 17:30:58 as along with 1 person choonpeng
	BIOCHEMISTRY: How Do Proteins Interact? [My Copy] Science, Vol. 320, No. 5882. (13 June 2008), pp. 1429-1430. by David D. Boehr, Peter E. Wright posted to docking pka protein_ligand by boris_aguilar on 2009-01-26 17:26:43 as along with 6 people victorclaessen reyez dchughes dullhunk paulschlesinger higueruelo
	Charge optimization leads to favorable electrostatic binding free energy [My Copy] Physical Review E, Vol. 59, No. 5. (1 May 1999), 5958. by Erik Kangas, Bruce Tidor posted to electrostatics pka protein_ligand by onufriev on 2009-01-23 23:58:35 as along with 1 person boris_aguilar
	Protein Structural Change Upon Ligand Binding: Linear Response Theory [My Copy] Physical Review Letters, Vol. 94, No. 7. (2005) by Mitsunori Ikeguchi, Jiro Ueno, Miwa Sato, Akinori Kidera posted to electrostatics pka protein_ligand by onufriev on 2009-01-23 23:57:13 as along with 3 people boris_aguilar apaydin aqeel
	Electrostatic contributions to protein-protein binding affinities: Application to Rap/Raf interaction [My Copy] Proteins: Structure, Function, and Genetics, Vol. 30, No. 4. (1998), pp. 407-423. by Ingo Muegge, Thomas Schweins, Arieh Warshel posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-23 23:43:34 as
	A hot spot of binding energy in a hormone-receptor interface. [My Copy] Science, Vol. 267, No. 5196. (20 January 1995), pp. 383-386. by T. Clackson, J. A. Wells posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-23 23:36:26 as along with 1 person bicko
	Principles of protein-protein interactions [My Copy] Proceedings of the National Academy of Sciences of the United States of America In Proceedings of the National Academy of Sciences of the United States of America, Vol. 93, No. 1. (9 January 1996), pp. 13-20. by S. Jones, J. M. Thornton posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-23 23:30:14 as along with 8 people dfdong mgomes sergiun joseolucha bicko chad_davis Evangelia iris_2001
	Conservation of polar residues as hot spots at protein interfaces [My Copy] Proteins: Structure, Function, and Genetics, Vol. 39, No. 4. (2000), pp. 331-342. by Zengjian Hu, Buyong Ma, Haim Wolfson, Ruth Nussinov posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-23 22:48:00 as along with 1 person timg
	Structural Characterisation and Functional Significance of Transient Protein-Protein Interactions [My Copy] Journal of Molecular Biology, Vol. 325, No. 5. (31 January 2003), pp. 991-1018. by Irene M. Nooren, Janet M. Thornton posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-23 22:45:45 as along with 1 person Evangelia
	Predicted protein-protein interaction sites from local sequence information [My Copy] FEBS Letters, Vol. 544, No. 1-3. (5 June 2003), pp. 236-239. by Yanay Ofran, Burkhard Rost posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-23 22:33:10 as along with 1 person cjeans
	Statistical analysis and prediction of protein-protein interfaces [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 60, No. 3. (19 May 2005), pp. 353-366. by Andrew J. Bordner, Ruben Abagyan posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-23 22:29:44 as along with 8 people and 2 groups dfdong barry bicko lyongu ameetsoni cjeans Evangelia marti structural_bioinformatics Bioinformatics
	Computer Simulation of Protein-Protein Interactions [My Copy] J. Phys. Chem. B, Vol. 105, No. 8. (1 March 2001), pp. 1504-1518. by A. H. Elcock, D. Sept, J. A. Mccammon posted to drug_design pka protein_ligand by boris_aguilar on 2009-01-23 22:16:17 as along with 1 person ima
	On the Role of Electrostatic Interactions in the Design of Protein–Protein Interfaces [My Copy] Journal of Molecular Biology, Vol. 318, No. 1. (19 April 2002), pp. 161-177. by F. Sheinerman posted to docking drug_design protein_ligand by boris_aguilar on 2009-01-23 22:10:19 as along with 3 people flbarroso carlescorbi higueruelo
	Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model [My Copy] Journal of the American Chemical Society, Vol. 121, No. 35. (1 September 1999), pp. 8033-8043. by Xiaoqin Zou, Yaxiong, Irwin D. Kuntz posted to gb protein_ligand by onufriev on 2008-11-04 23:52:20 as along with 1 person nickolay
	DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases [My Copy] Journal of Computer-Aided Molecular Design (May 2001), pp. 411-428. by T. J. A. Ewing, S. Makino, A. G. Skillman, I. D. Kuntz posted to protein_ligand by onufriev on 2008-11-02 02:10:12 as
	Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. [My Copy] Journal of computational chemistry, Vol. 25, No. 2. (30 January 2004), pp. 238-250. by H. Gohlke, D. A. Case posted to gb protein_ligand by onufriev on 2008-11-02 00:40:27 as along with 3 people flbarroso bmduggan lillekatt
	Molecular Forces in Antibody Maturation [My Copy] Physical Review Letters, Vol. 95, No. 20. (2005) by Melik C. Demirel, Arthur M. Lesk posted to molecular_geometry protein_ligand protein_mechanics by boris_aguilar on 2008-10-30 22:59:42 as
	2D depiction of nonbonding interactions for protein complexes. [My Copy] Journal of computational chemistry (22 October 2008) by Peng Zhou, Feifei Tian, Zhicai Shang posted to bioinf_methods protein_ligand protein_protein by barry on 2008-10-25 17:59:22 as along with 2 people and 3 groups whitead higueruelo Jiang Research Group structural_bioinformatics McCammon
	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 to pka protein_ligand by onufriev on 2008-10-15 15:00:16 as along with 6 people and 3 groups flbarroso csrocha bicko sobolevnrm RamuAnandakrishnan barry baker-group structural_bioinformatics McCammon
	Electrostatics of Ligand Binding: Parametrization of the Generalized Born Model and Comparison with the Poisson−Boltzmann Approach [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 18. (1 May 2006), pp. 9304-9313. by Hao-Yang Liu, Xiaoqin Zou posted to gb protein_electrostatics protein_ligand by onufriev on 2008-09-11 20:34:27 as along with 2 people nickolay flbarroso

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