dfgreen's ligand [46 articles] Export

Recent papers added to dfgreen's library classified by the tag ligand. You can also see everyone's ligand.

	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 to design docking ligand by dfgreen on 2009-01-09 02:59:20 as along with 3 people Diego_Prada BragilMassoud kazemi
	Computer design of bioactive molecules: a method for receptor-based de novo ligand design. [My Copy] Proteins, Vol. 11, No. 4. (1991), pp. 314-328. by J. B. Moon, W. J. Howe posted to design ligand by dfgreen on 2009-01-09 02:58:16 as
	Utility of homology models in the drug discovery process. [My Copy] Drug discovery today, Vol. 9, No. 15. (1 August 2004), pp. 659-669. by A. Hillisch, L. F. Pineda, R. Hilgenfeld posted to design homology ligand review by dfgreen on 2009-01-09 02:56:20 as
	Homology-based modelling of targets for rational drug design. [My Copy] Mini Rev Med Chem, Vol. 4, No. 7. (September 2004), pp. 793-804. by H. Wieman, K. Tøndel, E. Anderssen, F. Drabløs posted to design homology ligand review by dfgreen on 2009-01-09 02:54:57 as along with 1 person and 2 groups sangeetha Bioinformatics insilicodrug
	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
	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
	A Ligand That Is Predicted to Bind Better to Avidin than Biotin: Insights from Computational Fluorine Scanning [My Copy] Journal of the American Chemical Society, Vol. 122, No. 16. (1 April 2000), pp. 3909-3916. by Bernd Kuhn, Peter A. Kollman posted to design dynamics electrostatics ligand molecular by dfgreen on 2009-01-08 18:37:36 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
	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
	Optimization and Computational Evaluation of a Series of Potential Active Site Inhibitors of the V82F/I84V Drug-resistant Mutant of HIV-1 Protease: an Application of the Relaxed Complex Method of Structure-based Drug Design [My Copy] Chemical Biology & Drug Design, Vol. 67, No. 5. (2006), pp. 336-345. by Alexander L. Perryman, Jung-Hsin Lin, J. A. Mccammon posted to design docking ligand by dfgreen on 2009-01-08 13:15:04 as along with 1 person aqeel
	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
	Forces and energetics of hapten-antibody dissociation: a biased molecular dynamics simulation study. [My Copy] Journal of molecular biology, Vol. 314, No. 3. (30 November 2001), pp. 589-605. by E. Paci, A. Caflisch, A. Plückthun, M. Karplus posted to dissociation dynamics ligand molecular by dfgreen on 2009-01-08 03:04:03 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
	Theoretical Studies Suggest a New Antifolate as a More Potent Inhibitor of Thymidylate Synthase [My Copy] Journal of the American Chemical Society, Vol. 122, No. 18. (1 May 2000), pp. 4385-4393. by Tai-Sung Lee, Peter A. Kollman posted to design dynamics free-energy ligand molecular perturbation by dfgreen on 2009-01-08 02:39:43 as
	Evolutionary algorithms in computer-aided molecular design. [My Copy] Journal of computer-aided molecular design, Vol. 10, No. 4. (August 1996), pp. 337-358. by D. E. Clark, D. R. Westhead posted to design ligand review by dfgreen on 2009-01-08 02:37:54 as
	Computational molecular modeling in peptide drug design. [My Copy] International journal of peptide and protein research, Vol. 44, No. 6. (December 1994), pp. 513-531. by G. V. Nikiforovich posted to design ligand review by dfgreen on 2009-01-08 02:35:13 as
	HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site. [My Copy] Proteins, Vol. 19, No. 3. (July 1994), pp. 199-221. by M. B. Eisen, D. C. Wiley, M. Karplus, R. E. Hubbard posted to design ligand by dfgreen on 2009-01-08 02:32:22 as
	Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs. [My Copy] Proteins, Vol. 29, No. 1. (September 1997), pp. 32-58. by D. Joseph-McCarthy, J. M. Hogle, M. Karplus posted to design ligand by dfgreen on 2009-01-08 02:30:51 as
	Molecular recognition analyzed by docking simulations: the aspartate receptor and isocitrate dehydrogenase from Escherichia coli [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 90, No. 4. (15 February 1993), pp. 1146-1153. by B. L. Stoddard, D. E. Koshland posted to docking ligand by dfgreen on 2009-01-08 02:27:15 as
	Automated site-directed drug design using molecular lattices. [My Copy] Journal of molecular graphics, Vol. 10, No. 2. (June 1992) by R. A. Lewis, D. C. Roe, C. Huang, T. E. Ferrin, R. Langridge, I. D. Kuntz posted to design ligand by dfgreen on 2009-01-08 02:24:53 as
	Functionality maps of binding sites: a multiple copy simultaneous search method. [My Copy] Proteins, Vol. 11, No. 1. (1991), pp. 29-34. by A. Miranker, M. Karplus posted to design interactions ligand molecular by dfgreen on 2009-01-08 02:23:03 as along with 1 person ubcg08l
	CAVEAT: a program to facilitate the design of organic molecules. [My Copy] Journal of computer-aided molecular design, Vol. 8, No. 1. (February 1994), pp. 51-66. by G. Lauri, P. A. Bartlett posted to design ligand by dfgreen on 2009-01-08 02:21:39 as
	BUILDER v.2: improving the chemistry of a de novo design strategy. [My Copy] Journal of computer-aided molecular design, Vol. 9, No. 3. (June 1995), pp. 269-282. by D. C. Roe, I. D. Kuntz posted to design ligand by dfgreen on 2009-01-08 02:19:59 as
	Current methods for site-directed structure generation. [My Copy] J Comput Aided Mol Des, Vol. 8, No. 4. (August 1994), pp. 467-475. by R. A. Lewis, A. R. Leach posted to design ligand review by dfgreen on 2009-01-08 02:18:38 as along with 1 person peprovy
	The computer program LUDI: a new method for the de novo design of enzyme inhibitors. [My Copy] Journal of computer-aided molecular design, Vol. 6, No. 1. (February 1992), pp. 61-78. by H. J. Böhm posted to design ligand by dfgreen on 2009-01-08 02:17:37 as
	LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. [My Copy] Journal of computer-aided molecular design, Vol. 6, No. 6. (December 1992), pp. 593-606. by H. J. Böhm posted to design ligand by dfgreen on 2009-01-08 02:16:41 as
	An automated method for dynamic ligand design. [My Copy] Proteins, Vol. 23, No. 4. (December 1995), pp. 472-490. by A. Miranker, M. Karplus posted to design ligand by dfgreen on 2009-01-08 02:14:29 as along with 2 people and 1 group klexa oteri Structural Biology Group TorVergata
	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
	Improving Docking Accuracy through Molecular Mechanics Generalized Born Optimization and Scoring [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 3. (1 May 2007), pp. 1106-1119. by Matthew R. Lee, Yaxiong Sun posted to docking generalized-born ligand by dfgreen on 2009-01-08 01:59:47 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
	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
	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
	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

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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
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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
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dfgreen's ligand [46 articles] Export

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