boris_aguilar's library 77 articles Export

	Combining a polarizable force-field and a coarse-grained polarizable solvent model: Application to long dynamics simulations of bovine pancreatic trypsin inhibitor [My Copy] Journal of Computational Chemistry, Vol. 29, No. 11. (2008), pp. 1707-1724. by Michel Masella, Daniel Borgis, Philippe Cuniasse posted to implicit_solvation coarse_grain by boris_aguilar on 2009-11-05 22:14:29 as along with 2 people middledomain sunhwan
	Representing thermal vibrations and uncertainty in molecular surfaces [My Copy] In Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, Vol. 4665 (March 2002), pp. 80-90. by C. H. Lee, A. Varshney edited by R.~F.~Erbacher, P.~C.~Chen, M.~Groehn, J.~C.~Roberts, & C.~M.~Wittenbrink posted to surface molecular_geometry general_interest by boris_aguilar on 2009-10-27 22:21:54 as
	A Comprehensive Analytical Treatment of Continuum Electrostatics [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 5. (1 January 1996), pp. 1578-1599. by Michael Schaefer, Martin Karplus posted to implicit_solvation analytical_electrostatics by boris_aguilar on 2009-10-27 22:12:46 as along with 1 person dfgreen
	Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Adi Dan, Yanay Ofran, Yossef Kliger posted to structure stru protein_mechanics molecular_geometry by boris_aguilar on 2009-09-30 20:20:09 as along with 1 person reyez
	Structural mechanisms for domain movements in proteins. [My Copy] Biochemistry, Vol. 33, No. 22. (7 June 1994), pp. 6739-6749. by M. Gerstein, A. M. Lesk, C. Chothia posted to structure protein_mechanics by boris_aguilar on 2009-09-30 20:15:19 as along with 3 people and 2 groups vktrfrnkl ana kazemi structural_bioinformatics Bioinformatics
	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 6 people and 1 group sobolevnrm klexa oteri bmduggan barry zwang McCammon
	Calculating the Protonation States of Proteins and Small Molecules: Implications to Ligand-Receptor Interactions [My Copy] Current Computer-Aided Drug Design, Vol. 4 (2008), pp. 169-179. by Rooplekha Mitra, Radhey Shyam, Indranil Mitra, Maria A. Miteva, Emil Alexov posted to protein_ligand protein_electrostatics pka by boris_aguilar on 2009-09-04 17:49:02 as
	RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Alexej Abyzov, Robert Bjornson, Mihali Felipe, Mark Gerstein posted to structure protein_mechanics molecular_geometry by boris_aguilar on 2009-08-27 02:34:16 as
	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 5 people and 1 group ahmetbakan apaydin anuragsethi jmccammon okapi McCammon
	Molecular surfaces on proteins via beta shapes [My Copy] Computer-Aided Design, Vol. 39, No. 12. (December 2007), pp. 1042-1057. by J. Ryu, R. Park, D. Kim posted to surface molecular_geometry by boris_aguilar on 2009-08-11 21:05:23 as
	Three-dimensional beta shapes [My Copy] Computer-Aided Design, Vol. 38, No. 11. (November 2006), pp. 1179-1191. by D. Kim, J. Seo, D. Kim, J. Ryu, C. Cho posted to surface molecular_geometry by boris_aguilar on 2009-08-11 21:01:31 as
	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
	Effective Born radii in the generalized Born approximation: the importance of being perfect. [My Copy] J Comput Chem, Vol. 23, No. 14. (15 November 2002), pp. 1297-1304. by A. Onufriev, D. A. Case, D. Bashford posted to analytical_electrostatics effective_radii gb by boris_aguilar on 2009-05-21 16:46:01 as along with 3 people Lombardo_7 ttjoseph Martin8223
	A summary of the measured pK values of the ionizable groups in folded proteins. [My Copy] Protein science : a publication of the Protein Society, Vol. 18, No. 1. (January 2009), pp. 247-251. by G. R. Grimsley, J. M. Scholtz, C. N. Pace posted to pka by boris_aguilar on 2009-05-21 00:23:59 as
	Exploring protein native states and large-scale conformational changes with a modified generalized born model. [My Copy] Proteins, Vol. 55, No. 2. (1 May 2004), pp. 383-394. by A. Onufriev, D. Bashford, D. A. Case posted to analytical_electrostatics effective_radii gb by boris_aguilar on 2009-05-20 00:01:47 as along with 3 people RamuAnandakrishnan allmensch choonpeng
	Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 27, No. 6. (2006), pp. 719-729. by Jana Chocholouscaronová, Michael Feig posted to gb implicit_solvation molecular_dynamics by boris_aguilar on 2009-05-19 16:24:02 as along with 1 person yxue
	Generalized Born Model with a Simple, Robust Molecular Volume Correction [My Copy] J. Chem. Theory Comput., Vol. 3, No. 1. (9 January 2007), pp. 156-169. by J. Mongan, C. Simmerling, J. A. Mccammon, D. A. Case, A. Onufriev posted to gb implicit_solvation by boris_aguilar on 2009-05-16 05:08:59 as along with 1 person RamuAnandakrishnan
	The Effect of a Peptide Helix Macrodipole on the pKa of an Asp Side Chain Carboxylate [My Copy] Journal of the American Chemical Society, Vol. 118, No. 48. (1 January 1996), pp. 12038-12044. by Hemant V. Joshi, Mark S. Meier posted to drug_design pka structure by boris_aguilar on 2009-03-31 23:05:26 as
	Predicting protein p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> by environment similarity [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Francesca Milletti, Loriano Storchi, Gabriele Cruciani posted to pka by boris_aguilar on 2009-02-26 15:34:18 as along with 1 person and 1 group sobolevnrm 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
	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
	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, 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
	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 drug_design pka protein_ligand by boris_aguilar on 2009-01-23 23:25:35 as along with 1 person onufriev
	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 drug_design pka protein_ligand by boris_aguilar on 2009-01-23 23:17:18 as along with 2 people chemrahul82 onufriev
	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
	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
	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 molecular_geometry protein_ligand protein_mechanics by boris_aguilar on 2008-10-30 22:58:03 as along with 3 people onufriev apaydin aqeel
	A protein-DNA docking benchmark [My Copy] Nucl. Acids Res., Vol. 36, No. 14. (1 August 2008), e88. by Marc van Dijk, Alexandre M. Bonvin posted to docking pka by boris_aguilar on 2008-08-19 21:44:41 as along with 4 people HawkinsJohnC oteri reyez neils
	A nonlinear elasticity model of macromolecular conformational change induced by electrostatic forces [My Copy] Journal of Mathematical Analysis and Applications, Vol. 340, No. 1. (1 April 2008), pp. 135-164. by Y. C. Zhou, Michael Holst, Andrew J. Mccammon posted to general_interest protein_electrostatics structure by boris_aguilar on 2008-08-18 16:31:01 as along with 1 person and 1 group sobolevnrm baker-group

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pka	43
drug_design	34
protein_ligand	33
structure	18
docking	15
ligand	9
protein_mechanics	8
molecular_geometry	7
implicit_solvation	6
gb	4
analytical_electrostatics	4
surface	3
general_interest	3
dna	3
effective_radii	2
protein_electrostatics	2
free_energy	2
poisson-boltzmann	2
stru	1
coarse_grain	1
biotechnology	1
molecular_dynamics	1

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