dfgreen's binding [39 articles] Export

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	Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis [My Copy] Proteins: Structure, Function, and Genetics, Vol. 4, No. 1. (1988), pp. 7-18. by Michael K. Gilson, Barry Honig posted to binding electrostatics poisson-boltzmann solvation by dfgreen on 2009-01-08 22:50:19 as along with 1 person flbarroso
	Macroscopic models of aqueous solutions: biological and chemical applications [My Copy] The Journal of Physical Chemistry, Vol. 97, No. 6. (1 February 1993), pp. 1101-1109. by Barry Honig, Kim Sharp, An S. Yang posted to binding electrostatics poisson-boltzmann protein by dfgreen on 2009-01-08 22:49:05 as
	The statistical-thermodynamic basis for computation of binding affinities: a critical review. [My Copy] Biophys J, Vol. 72, No. 3. (March 1997), pp. 1047-1069. by M. K. Gilson, J. A. Given, B. L. Bush, J. A. McCammon posted to binding free-energy ligand by dfgreen on 2009-01-08 20:57:03 as along with 3 people and 2 groups ssomani hmk cchang structure-bii Chang group
	BIOMOLECULAR SIMULATIONS: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions [My Copy] Annual Review of Biophysics and Biomolecular Structure, Vol. 30, No. 1. (2001), pp. 211-243. by Wei Wang, Oreola Donini, Carolina M. Reyes, Peter A. Kollman posted to binding catalysis dna dynamics enzyme ligand molecular protein review by dfgreen on 2009-01-08 19:05:43 as along with 5 people nickolay flbarroso bmduggan RamuAnandakrishnan ibuch
	Poisson-Boltzmann analysis of the lambda repressor-operator interaction. [My Copy] Biophysical journal, Vol. 63, No. 5. (November 1992), pp. 1280-1285. by M. Zacharias, B. A. Luty, M. E. Davis, J. A. McCammon posted to binding dna electrostatics protein by dfgreen on 2009-01-08 18:46:48 as along with 1 person flbarroso
	Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations. [My Copy] Journal of molecular biology, Vol. 275, No. 5. (6 February 1998), pp. 823-846. by G. Archontis, T. Simonson, D. Moras, M. Karplus posted to binding dynamics electrostatics free-energy ligand molecular perturbation specificity by dfgreen on 2009-01-08 18:44:47 as
	A Poisson−Boltzmann Study of Charge Insertion in an Enzyme Active Site: The Effect of Dielectric Relaxation [My Copy] The Journal of Physical Chemistry B, Vol. 103, No. 29. (1 July 1999), pp. 6142-6156. by Thomas Simonson, Georgios Archontis, Martin Karplus posted to binding dynamics electrostatics ligand molecular by dfgreen on 2009-01-08 18:41:34 as
	Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase, [My Copy] Journal of Molecular Biology, Vol. 306, No. 2. (16 February 2001), pp. 307-327. by Georgios Archontis, Thomas Simonson, Martin Karplus posted to binding dynamics electrostatics ligand molecular by dfgreen on 2009-01-08 18:24:24 as along with 2 people flbarroso dmobley
	Optimization of electrostatic binding free energy [My Copy] The Journal of Chemical Physics, Vol. 106, No. 21. (1997), pp. 8681-8690. by Lee P. Lee, Bruce Tidor posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 17:34:16 as
	Electrostatic specificity in molecular ligand design [My Copy] The Journal of Chemical Physics, Vol. 112, No. 20. (2000), pp. 9120-9131. by Erik Kangas, Bruce Tidor posted to binding electrostatics ligand optimization specificity by dfgreen on 2009-01-08 17:32:10 as
	Optimizing electrostatic affinity in ligand--receptor binding: Theory, computation, and ligand properties [My Copy] The Journal of Chemical Physics, Vol. 109, No. 17. (1998), pp. 7522-7545. by Erik Kangas, Bruce Tidor posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 17:28:02 as
	Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant. [My Copy] Journal of molecular biology, Vol. 236, No. 4. (4 March 1994), pp. 1049-1066. by F. T. Lau, M. Karplus posted to binding dynamics free-energy ligand molecular perturbation by dfgreen on 2009-01-08 17:23:12 as
	Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. [My Copy] Journal of molecular biology, Vol. 297, No. 5. (14 April 2000), pp. 1145-1158. by C. M. Reyes, P. A. Kollman posted to binding dynamics free-energy molecular perturbation rna-protein by dfgreen on 2009-01-08 17:19:42 as along with 2 people balewis bmduggan
	Optimizing Ligand Charges for Maximum Binding Affinity. A Solvated Interaction Energy Approach [My Copy] The Journal of Physical Chemistry B, Vol. 105, No. 4. (1 February 2001), pp. 889-899. by Traian Sulea, Enrico O. Purisima posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 14:10:50 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 binding electrostatics ligand optimization by dfgreen on 2009-01-08 13:12:44 as along with 1 person boris_aguilar
	Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study. [My Copy] Proteins, Vol. 34, No. 1. (1 January 1999), pp. 69-81. by J. Wang, R. Dixon, P. A. Kollman posted to binding dynamics ligand molecular by dfgreen on 2009-01-08 13:03:39 as
	The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors. [My Copy] Journal of computer-aided molecular design, Vol. 12, No. 3. (May 1998), pp. 215-227. by R. J. Radmer, P. A. Kollman posted to binding design free-energy ligand perturbation by dfgreen on 2009-01-08 02:56:43 as
	Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations. [My Copy] Journal of computer-aided molecular design, Vol. 13, No. 2. (March 1999), pp. 109-121. by M. A. McCarrick, P. A. Kollman posted to binding dynamics free-energy ligand molecular perturbation by dfgreen on 2009-01-08 02:54:30 as
	Electrostatic Influence on the Kinetics of Ligand Binding to Acetylcholinesterase. DISTINCTIONS BETWEEN ACTIVE CENTER LIGANDS AND FASCICULIN [My Copy] J. Biol. Chem., Vol. 272, No. 37. (12 September 1997), pp. 23265-23277. by Zoran Radic, Paul D. Kirchhoff, Daniel M. Quinn, Andrew J. Mccammon, Palmer Taylor posted to binding electrostatics kinetics ligand by dfgreen on 2009-01-08 02:10:02 as
	Binding of antifusion peptides with HIVgp41 from molecular dynamics simulations: quantitative correlation with experiment. [My Copy] Proteins, Vol. 67, No. 3. (15 May 2007), pp. 630-642. by B. Strockbine, R. C. Rizzo posted to binding dynamics generalized-born ligand molecular by dfgreen on 2009-01-08 01:56:17 as
	Design of Mutation-resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis [My Copy] Chemical Biology & Drug Design, Vol. 69, No. 5. (May 2007), pp. 298-313. by Sripriya Chellappan, Kiran Kumar Reddy, Akbar Ali, et al.Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Visvaldas Kairys, Miguel X. Fernandes, Michael D. Altman, Bruce Tidor, Tariq M. Rana, Celia A. Schiffer, Michael K. Gilson posted to binding design ligand resistance by dfgreen on 2009-01-08 01:53:07 as along with 1 person and 1 group cdppublications CDP
	The Contribution of Vibrational Entropy to Molecular Association : The Dimerization of Insulin [My Copy] Journal of Molecular Biology, Vol. 238, No. 3. (5 May 1994), pp. 405-414. by Bruce Tidor, Martin Karplus posted to binding entropy harmonics protein vibrational by dfgreen on 2009-01-08 01:46:57 as along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
	Barstar is electrostatically optimized for tight binding to barnase. [My Copy] Nature structural biology, Vol. 8, No. 1. (January 2001), pp. 73-76. by L. P. Lee, B. Tidor posted to binding electrostatics interactions optimization protein protein-protein by dfgreen on 2009-01-08 01:40:32 as along with 1 person flbarroso
	How optimal are the binding energetics of barnase and barstar? [My Copy] Biophysical journal, Vol. 87, No. 3. (September 2004), pp. 1618-1630. by T. Wang, S. Tomic, R. R. Gabdoulline, R. C. Wade posted to binding electrostatics interactions protein protein-protein by dfgreen on 2009-01-08 01:38:41 as along with 3 people flbarroso chad_davis ras
	Computational design of antibody-affinity improvement beyond in vivo maturation. [My Copy] Nat Biotechnol (23 September 2007) by Shaun M M. Lippow, K Dane D. Wittrup, Bruce Tidor posted to binding design electrostatics interactions protein protein-protein by dfgreen on 2009-01-08 01:33:59 as along with 4 people and 1 group Scis0000002 kirasato hmk zwang Chang group
	Escherichia coli Glutaminyl-tRNA Synthetase is Electrostatically Optimized for Binding of its Cognate Substrates [My Copy] Journal of Molecular Biology, Vol. 342, No. 2. (10 September 2004), pp. 435-452. by D. F. Green, B. Tidor posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 01:19:42 as
	Computation of electrostatic complements to proteins: a case of charge stabilized binding. [My Copy] Protein science : a publication of the Protein Society, Vol. 7, No. 1. (January 1998), pp. 206-210. by L. T. Chong, S. E. Dempster, Z. S. Hendsch, L. P. Lee, B. Tidor posted to binding electrostatics optimization protein by dfgreen on 2009-01-08 01:14:58 as
	Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding. [My Copy] Protein science : a publication of the Protein Society, Vol. 8, No. 7. (July 1999), pp. 1381-1392. by Z. S. Hendsch, B. Tidor posted to binding electrostatics interactions protein protein-protein by dfgreen on 2009-01-08 01:13:00 as
	Charge optimization leads to favorable electrostatic binding free energy. [My Copy] Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, Vol. 59, No. 5 Pt B. (May 1999), pp. 5958-5961. by E. Kangas, B. Tidor posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 01:11:00 as along with 1 person flbarroso
	Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex. [My Copy] Protein science : a publication of the Protein Society, Vol. 10, No. 2. (February 2001), pp. 362-377. by L. P. Lee, B. Tidor posted to binding electrostatics optimization protein by dfgreen on 2009-01-07 23:35:10 as along with 2 people flbarroso ras
	Optimization of electrostatic interactions in protein-protein complexes. [My Copy] Biophysical journal, Vol. 93, No. 10. (15 November 2007), pp. 3340-3352. by K. Brock, K. Talley, K. Coley, P. Kundrotas, E. Alexov posted to binding electrostatics interactions optimization protein-protein by dfgreen on 2009-01-07 23:33:15 as along with 4 people and 1 group flbarroso timg choonpeng sobolevnrm baker-group
	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 binding electrostatics optimization protein by dfgreen on 2009-01-07 23:24:29 as along with 1 person boris_aguilar
	Action-at-a-distance interactions enhance protein binding affinity. [My Copy] Protein science : a publication of the Protein Society, Vol. 14, No. 5. (May 2005), pp. 1363-1369. by B. A. Joughin, D. F. Green, B. Tidor posted to action-at-a-distance binding electrostatics protein by dfgreen on 2009-01-07 23:19:09 as along with 1 person Lombardo_7
	Computational models explain the oligosaccharide specificity of cyanovirin-N. [My Copy] Protein science : a publication of the Protein Society, Vol. 17, No. 11. (November 2008), pp. 2008-2014. by Y. K. Fujimoto, R. N. Terbush, V. Patsalo, D. F. Green posted to binding carbohydrate electrostatics ligand specificity by dfgreen on 2009-01-07 20:24:42 as
	Electrostatic Complementarity at Ligand Binding Sites: Application to Chorismate Mutase [My Copy] J. Phys. Chem. B, Vol. 105, No. 4. (1 February 2001), pp. 880-888. by E. Kangas, B. Tidor posted to binding electrostatics ligand optimization by dfgreen on 2009-01-07 20:11:32 as along with 1 person dimka
	Charge Optimization Increases the Potency and Selectivity of a Chorismate Mutase Inhibitor [My Copy] Journal of the American Chemical Society, Vol. 125, No. 19. (1 May 2003), pp. 5598-5599. by Ajay Mandal, Donald Hilvert posted to binding electrostatics ligand optimization by dfgreen on 2009-01-07 19:46:07 as
	Optimizing Molecular Electrostatic Interactions: Binding Affinity and Specificity [My Copy] (June 2000) by Erik Kangas posted to binding electrostatics ligand specificity by dfgreen on 2009-01-07 18:52:29 as
	Binding affinity and specificity from computational studies [My Copy] Curr. Org. Chem., Vol. 6 (2002), pp. 1319-1332. by T. Lazaridis posted to binding ligand specificity by dfgreen on 2009-01-07 18:52:25 as
	Evaluation of electrostatic interactions [My Copy] In Current Protocols in Bioinformatics (2003) by David F. Green, Bruce Tidor edited by G. E. Petsko posted to binding electrostatics optimization by dfgreen on 2009-01-07 18:52:02 as

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file-import-09-01-07b	274
electrostatics	96
protein	90
design	63
dynamics	47
molecular	47
ligand	46
solvation	44
binding	39
packing	19
quantum-mechanics	19
charges	18
optimization	18
free-energy	17
interactions	17
pka	17
review	17
perturbation	16
ab-initio	15
force-fields	15
generalized-born	13
hydrophobic	13
engineering	11
protein-protein	11
software	11
specificity	9
stability	9
poisson-boltzmann	7
structure	7
biopharmaceuticals	6
carbohydrate	6
conformational	6
docking	5
enzyme	5
biology	4
catalysis	4
dna	4
homology	4
preferences	4
sequence	4
systems	4
entropy	3
kinetics	3
linear-programming	3
quadratic-programming	3
semi-empirical	3
continuum-vdw	2
monte-carlo	2
protonation	2
rna	2
structure-prediction	2
visualization	2
water	2
action-at-a-distance	1
allostery	1
analysis	1
atp	1
brownian	1
calmodulin	1
dissociation	1
effect	1
electrochemistry	1
folding	1
g-protein	1
harmonics	1
hierarchicies	1
mean-field	1
membrane-association	1
phylogeny	1
proteomics	1
resistance	1
rna-protein	1
senstivity	1
text	1
vibrational	1

dfgreen's binding [39 articles] Export

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