dfgreen's molecular [47 articles] Export

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	Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations [My Copy] The Journal of Chemical Physics, Vol. 100, No. 12. (1994), pp. 9050-9063. by Dmitrii Beglov, Benoît Roux posted to dynamics molecular solvation by dfgreen on 2009-01-08 23:07:33 as along with 2 people dmitry_s_yershov jwagoner
	Scalable molecular dynamics with NAMD [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (December 2005), pp. 1781-1802. by James C. Phillips, Rosemary Braun, Wei Wang, et al.James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten posted to dynamics molecular software by dfgreen on 2009-01-08 22:55:21 as along with 20 people and 5 groups krapnik pjkiley flbarroso yxue r2s2 grondina rpetrenko oteri oceanwind vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros sobolevnrm ibuch Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group
	CHARMM: A program for macromolecular energy, minimization, and dynamics calculations [My Copy] Journal of Computational Chemistry, Vol. 4, No. 2. (1983), pp. 187-217. by Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, Martin Karplus posted to dynamics force-fields molecular software by dfgreen on 2009-01-08 22:40:53 as along with 16 people ubcg08l flbarroso nickolay newton1234 kgutwin r2s2 rpetrenko oceanwind RamuAnandakrishnan tovrstra Lombardo_7 dgront mmuecke rabio saravan gisle
	Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry [My Copy] Angewandte Chemie International Edition in English, Vol. 29, No. 9. (1990), pp. 992-1023. by Wilfred F. van Gunsteren, Herman J. C. Berendsen posted to dynamics molecular review by dfgreen on 2009-01-08 22:33:06 as along with 2 people flbarroso karinaecomp
	Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area [My Copy] The Journal of Physical Chemistry, Vol. 99, No. 9. (1 March 1995), pp. 2885-2892. by A. Wallqvist, B. J. Berne posted to dynamics hydrophobic molecular solvation by dfgreen on 2009-01-08 20:39:24 as
	Molecular dynamics of ferrocytochrome c. [My Copy] Nature, Vol. 286, No. 5770. (17 July 1980), pp. 304-305. by S. H. Northrup, M. R. Pear, J. A. McCammon, M. Karplus posted to dynamics molecular by dfgreen on 2009-01-08 19:58:07 as
	Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials [My Copy] The Journal of Physical Chemistry, Vol. 99, No. 29. (1 July 1995), pp. 11575-11583. by Yanbo Ding, Dan N. Bernardo, Karsten Krogh-Jespersen, Ronald M. Levy posted to dynamics free-energy molecular perturbation solvation by dfgreen on 2009-01-08 19:54:00 as
	Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution. [My Copy] Proc Natl Acad Sci U S A, Vol. 92, No. 4. (14 February 1995), pp. 1082-1086. by T. Simonson, D. Perahia posted to dynamics electrostatics molecular protein by dfgreen on 2009-01-08 19:16:49 as along with 2 people chiufanlee onufriev
	Electrostatics in biomolecular structure and dynamics [My Copy] Chemical Reviews, Vol. 90, No. 3. (1 May 1990), pp. 509-521. by Malcolm E. Davis, J. Andrew Mccammon posted to dynamics electrostatics molecular protein review by dfgreen on 2009-01-08 19:08:08 as along with 2 people scampos flbarroso
	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
	Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations [My Copy] The Journal of Physical Chemistry, Vol. 97, No. 9. (1 March 1993), pp. 2009-2014. by Paul E. Smith, Roger M. Brunne, Alan E. Mark, Wilfred F. Van Gunsteren posted to dynamics electrostatics molecular by dfgreen on 2009-01-08 18:50:28 as
	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
	Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure. [My Copy] Proteins, Vol. 33, No. 2. (1 November 1998), pp. 145-158. by H. W. van Vlijmen, M. Schaefer, M. Karplus posted to dynamics electrostatics molecular pka protein by dfgreen on 2009-01-08 18:09:25 as along with 2 people franklu310 RamuAnandakrishnan
	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
	Molecular dynamics simulations in biology [My Copy] Nature, Vol. 347, No. 6294. (18 October 1990), pp. 631-639. by Martin Karplus, Gregory A. Petsko posted to dynamics molecular review by dfgreen on 2009-01-08 17:40:10 as
	Internal motions of antibody molecules. [My Copy] Nature, Vol. 268, No. 5622. (25 August 1977), pp. 765-766. by J. A. McCammon, M. Karplus posted to dynamics molecular by dfgreen on 2009-01-08 17:38:20 as
	Protein structural fluctuations during a period of 100 ps. [My Copy] Nature, Vol. 277, No. 5697. (15 February 1979) by M. Karplus, J. A. McCammon posted to dynamics molecular by dfgreen on 2009-01-08 17:37:14 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
	Active site dynamics of ribonuclease [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 82, No. 24. (December 1985), pp. 8458-8462. by A. T. Brünger, C. L. Brooks, M. Karplus posted to dynamics molecular by dfgreen on 2009-01-08 14:08:16 as
	Hidden thermodynamics of mutant proteins: a molecular dynamics analysis [My Copy] Science, Vol. 244, No. 4908. (2 June 1989), pp. 1069-1072. by J. Gao, K. Kuczera, B. Tidor, M. Karplus posted to dynamics free-energy molecular perturbation protein stability by dfgreen on 2009-01-08 14:04:19 as
	Free energy of sickling: A simulation analysis [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 87, No. 21. (November 1990), pp. 8481-8485. by K. Kuczera, J. Gao, B. Tidor, M. Karplus posted to dynamics free-energy molecular perturbation by dfgreen on 2009-01-08 14:01:43 as
	Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 88, No. 23. (1 December 1991), pp. 10880-10884. by M. Prevost, S. J. Wodak, B. Tidor, M. Karplus posted to dynamics effect hydrophobic molecular protein stability by dfgreen on 2009-01-08 13:59:36 as
	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
	Dynamics of folded proteins. [My Copy] Nature, Vol. 267, No. 5612. (16 June 1977), pp. 585-590. by J. A. McCammon, B. R. Gelin, M. Karplus posted to dynamics molecular by dfgreen on 2009-01-08 13:04:54 as along with 1 person LamBras
	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 hinge-bending mode in lysozyme. [My Copy] Nature, Vol. 262, No. 5566. (22 July 1976), pp. 325-326. by J. A. McCammon, B. R. Gelin, M. Karplus, P. G. Wolynes posted to dynamics molecular by dfgreen on 2009-01-08 03:18:58 as along with 1 person aqeel
	A dynamic model for the allosteric mechanism of GroEL. [My Copy] J Mol Biol, Vol. 302, No. 2. (15 September 2000), pp. 303-313. by J. Ma, P. B. Sigler, Z. Xu, M. Karplus posted to allostery dynamics molecular by dfgreen on 2009-01-08 03:17:25 as along with 3 people lna dgront LamBras
	Picosecond dynamics of tyrosine side chains in proteins [My Copy] Biochemistry, Vol. 18, No. 6. (1 March 1979), pp. 927-942. by Andrew J. Mccammon, Peter G. Wolynes, Martin Karplus posted to dynamics molecular by dfgreen on 2009-01-08 03:13:43 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
	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
	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
	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
	Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability. [My Copy] Journal of molecular biology, Vol. 285, No. 4. (29 January 1999), pp. 1811-1830. by P. I. de Bakker, P. H. Hünenberger, J. A. McCammon posted to dynamics electrostatics molecular protein stability by dfgreen on 2009-01-08 02:08:55 as
	RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. [My Copy] Journal of molecular biology, Vol. 317, No. 4. (5 April 2002), pp. 493-506. by E. J. Sorin, M. A. Engelhardt, D. Herschlag, V. S. Pande posted to dynamics folding molecular rna by dfgreen on 2009-01-08 02:05:33 as
	Parametrization of a Generalized Born/Solvent-Accessible Surface Area Model and Applications to the Simulation of Protein Dynamics [My Copy] The Journal of Physical Chemistry B, Vol. 106, No. 18. (1 May 2002), pp. 4844-4853. by Jiang Zhu, Yunyu Shi, Haiyan Liu posted to dynamics generalized-born molecular by dfgreen on 2009-01-08 02:02:33 as
	Implicit Solvent Simulations of DNA and DNA-Protein Complexes: Agreement with Explicit Solvent vs Experiment [My Copy] J. Phys. Chem. B, Vol. 110, No. 34. (31 August 2006), pp. 17240-17251. by J. Chocholousova, M. Feig posted to dynamics generalized-born molecular by dfgreen on 2009-01-08 02:01:09 as along with 1 person Elena_Zubova
	HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 4. (24 January 2006), pp. 915-920. by V. Hornak, A. Okur, R. C. Rizzo, C. Simmerling posted to dynamics molecular by dfgreen on 2009-01-08 01:57:32 as along with 3 people aqeel allmensch RamuAnandakrishnan
	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
	Simulation analysis of the stability mutant R96H of T4 lysozyme [My Copy] Biochemistry, Vol. 30, No. 13. (1 April 1991), pp. 3217-3228. by Bruce Tidor, Martin Karplus posted to dynamics molecular protein stability by dfgreen on 2009-01-07 20:56:57 as
	Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin [My Copy] Science, Vol. 235, No. 4786. (16 January 1987), pp. 318-321. by R. Elber, M. Karplus posted to conformational dynamics entropy molecular by dfgreen on 2009-01-07 20:55:35 as along with 1 person ruvido

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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 molecular [47 articles] Export

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