dfgreen's Kollman:PA [27 articles] Export

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	A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model [My Copy] The Journal of Physical Chemistry, Vol. 97, No. 40. (1 October 1993), pp. 10269-10280. by Christopher I. Bayly, Piotr Cieplak, Wendy Cornell, Peter A. Kollman posted to ab-initio charges quantum-mechanics by dfgreen on 2009-01-09 02:00:35 as along with 2 people Scis0000002 paddydu
	An approach to computing electrostatic charges for molecules [My Copy] Journal of Computational Chemistry, Vol. 5, No. 2. (1984), pp. 129-145. by U. Chandra Singh, Peter A. Kollman posted to charges quantum-mechanics by dfgreen on 2009-01-08 23:38:08 as along with 4 people and 1 group whitead pavanghatty tovrstra kimikazu Jiang Research Group
	Atomic charges derived from semiempirical methods [My Copy] Journal of Computational Chemistry, Vol. 11, No. 4. (1990), pp. 431-439. by Brent H. Besler, Kenneth M. Merz, Peter A. Kollman posted to charges quantum-mechanics semi-empirical by dfgreen on 2009-01-08 23:36:06 as along with 1 person and 1 group A_Coletta_Thesis Structural Biology Group TorVergata
	A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules [My Copy] Journal of the American Chemical Society, Vol. 117, No. 19. (1 May 1995), pp. 5179-5197. by Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, et al.Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, Peter A. Kollman posted to force-fields by dfgreen on 2009-01-08 22:31:13 as along with 6 people Lombardo_7 softsimu coomteng flbarroso kgutwin pavanghatty
	A new force field for molecular mechanical simulation of nucleic acids and proteins [My Copy] Journal of the American Chemical Society, Vol. 106, No. 3. (1 February 1984), pp. 765-784. by Scott J. Weiner, Peter A. Kollman, David A. Case, et al.Chandra U. Singh, Caterina Ghio, Guliano Alagona, Salvatore Profeta, Paul Weiner posted to force-fields by dfgreen on 2009-01-08 22:30:27 as along with 1 person pavanghatty
	An all atom force field for simulations of proteins and nucleic acids [My Copy] Journal of Computational Chemistry, Vol. 7, No. 2. (1986), pp. 230-252. by Scott J. Weiner, Peter A. Kollman, Dzung T. Nguyen, David A. Case posted to force-fields by dfgreen on 2009-01-08 22:28:02 as along with 2 people allmensch Elena_Zubova
	THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 1011-1021. by Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, Peter A. Kollman posted to free-energy perturbation by dfgreen on 2009-01-08 21:59:26 as along with 11 people and 1 group jrperillaj edws Diego_Prada stephenbond A_Coletta_Thesis sunnytov dgront sikorski jwagoner bransfop allmensch Structural Biology Group TorVergata
	Solvation Free Energies of Amides and Amines: Disagreement between Free Energy Calculations and Experiment [My Copy] Journal of the American Chemical Society, Vol. 117, No. 22. (1 June 1995), pp. 6057-6063. by Pierre-Yves Morgantini, Peter A. Kollman posted to free-energy perturbation solvation by dfgreen on 2009-01-08 19:39:58 as
	Investigating the Anomalous Solvation Free Energies of Amines with a Polarizable Potential [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 6. (1 January 1996), pp. 2367-2371. by Elaine C. Meng, James W. Caldwell, Peter A. Kollman posted to force-fields solvation by dfgreen on 2009-01-08 19:36:19 as
	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
	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
	Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations [My Copy] Journal of Computational Chemistry, Vol. 25, No. 15. (2004), pp. 1865-1872. by Bernd Kuhn, Peter A. Kollman, Martin Stahl posted to dynamics electrostatics molecular pka protein by dfgreen on 2009-01-08 18:00:51 as along with 3 people and 1 group flbarroso sobolevnrm sim82 baker-group
	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
	Molecular dynamics simulations of active site mutants of triosephosphate isomerase [My Copy] Protein Eng., Vol. 3, No. 8. (1 August 1990), pp. 677-690. by Valerie Daggett, Peter A. Kollman posted to dynamics enzyme kinetics molecular by dfgreen on 2009-01-08 13:57:03 as
	Free energy calculations of the mutation of Ile96 -> Ala in barnase: contributions to the difference in stability [My Copy] Protein Eng., Vol. 9, No. 3. (1 March 1996), pp. 273-281. by Ying-Chieh Sun, David L. Veenstra, Peter A. Kollman posted to free-energy perturbation protein stability by dfgreen on 2009-01-08 13:54:23 as
	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
	Molecular dynamics simulations of "loop closing" in the enzyme triose phosphate isomerase. [My Copy] Journal of molecular biology, Vol. 198, No. 3. (5 December 1987), pp. 533-546. by F. K. Brown, P. A. Kollman posted to dynamics molecular by dfgreen on 2009-01-08 03:00:06 as
	A molecular dynamics simulation of double-helical B-DNA including counterions and water [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 82, No. 19. (October 1985), pp. 6537-6540. by G. L. Seibel, U. C. Singh, P. A. Kollman posted to dna dynamics molecular by dfgreen on 2009-01-08 02:57:55 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
	Insight into the specificity of thymidylate synthase from molecular dynamics and free energy perturbation calculations [My Copy] Journal of the American Chemical Society, Vol. 117, No. 27. (1 July 1995), pp. 7213-7227. by Giulio Rastelli, Bert Thomas, Peter A. Kollman, Daniel V. Santi posted to dynamics free-energy molecular perturbation specificity by dfgreen on 2009-01-08 02:51:59 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
	An Alternative Explanation for the Catalytic Proficiency of Orotidine 5‘-Phosphate Decarboxylase [My Copy] Journal of the American Chemical Society, Vol. 123, No. 51. (1 December 2001), pp. 12837-12848. by Tai-Sung Lee, Lillian T. Chong, John D. Chodera, Peter A. Kollman posted to catalysis enzyme by dfgreen on 2009-01-08 02:12:50 as
	Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis? [My Copy] The Journal of Physical Chemistry B, Vol. 106, No. 7. (1 February 2002), pp. 1537-1542. by Peter A. Kollman, Bernd Kuhn, Mikael Perakyla posted to catalysis enzyme by dfgreen on 2009-01-08 02:11:40 as
	Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices [My Copy] Journal of the American Chemical Society, Vol. 120 (1998), pp. 9401-9409. by J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, D. A. Case posted to file-import-09-01-07b by dfgreen on 2009-01-07 18:52:19 as
	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 (1999), pp. 8133-8143. by I. Massova, P. A. Kollman posted to file-import-09-01-07b by dfgreen on 2009-01-07 18:52:05 as
	Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece [My Copy] Proteins: Structure, Function, and Genetics, Vol. 39 (2000), pp. 309-316. by M. R. Lee, Y. Duan, P. A. Kollman posted to file-import-09-01-07b by dfgreen on 2009-01-07 18:52:05 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 Kollman:PA [27 articles] Export

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