dfgreen's Karplus:M [37 articles] Export

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	Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. [My Copy] Proteins, Vol. 4, No. 2. (1988), pp. 148-156. by A. T. Brünger, M. Karplus posted to interactions protonation software by dfgreen on 2009-01-08 22:59:43 as along with 1 person csrocha
	Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes. [My Copy] J Comput Chem, Vol. 22, No. 15. (30 November 2001), pp. 1857-1879. by Michael Schaefer, Christian Bartels, Fabrice Leclerc, Martin Karplus posted to electrostatics generalized-born by dfgreen on 2009-01-08 22:54:23 as along with 1 person baaden
	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 electrostatics generalized-born by dfgreen on 2009-01-08 22:53:34 as along with 1 person boris_aguilar
	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
	All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins† [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 18. (1 April 1998), pp. 3586-3616. by A. D. Mackerell, D. Bashford, M. Bellott, et al.R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-Mccarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus posted to force-fields by dfgreen on 2009-01-08 22:38:00 as along with 12 people jmparks dsmueller rpetrenko jrperillaj Diego_Prada oceanwind mkrishna timg dimka ttjoseph papatonyhill ssomani
	An all-atom empirical energy function for the simulation of nucleic acids [My Copy] Journal of the American Chemical Society, Vol. 117, No. 48. (1 December 1995), pp. 11946-11975. by Alexander D. Mackerell, Joanna Wiorkiewicz-Kuczera, Martin Karplus posted to force-fields by dfgreen on 2009-01-08 22:37:05 as
	Backbone-dependent rotamer library for proteins. Application to side-chain prediction. [My Copy] Journal of molecular biology, Vol. 230, No. 2. (20 March 1993), pp. 543-574. by R. L. Dunbrack, M. Karplus posted to packing protein structure by dfgreen on 2009-01-08 21:56:26 as along with 3 people and 1 group carlosjavierna nknii carlk TCR_Signaling
	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
	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
	Free Energy Simulations Come of Age: Protein−Ligand Recognition [My Copy] Accounts of Chemical Research, Vol. 35, No. 6. (1 June 2002), pp. 430-437. by Thomas Simonson, Georgios Archontis, Martin Karplus posted to no-tag by dfgreen on 2009-01-08 18:25:25 as along with 2 people flbarroso dmobley
	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
	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
	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
	pH-Dependence of Protein Stability: Absolute Electrostatic Free Energy Differences between Conformations [My Copy] J. Phys. Chem. B, Vol. 101, No. 9. (27 February 1997), pp. 1663-1683. by M. Schaefer, M. Sommer, M. Karplus posted to electrostatics pka protein by dfgreen on 2009-01-08 13:09:38 as along with 1 person yalexeev
	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
	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
	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
	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
	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
	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
	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
	Enhanced sampling in molecular dynamics: Use of the time-dependent Hartree apporximation for a simulation of carbon monoxide diffusion through myoglobin [My Copy] Journal of the American Chemical Society, Vol. 112 (1990), pp. 9161-9175. by R. Elber, M[artin] Karplus posted to file-import-09-01-07b by dfgreen on 2009-01-07 18:52:10 as
	Multiple copy simulateous search and construction of ligands in binding sites: Application to inhibitors of HIV-1 aspartic proteinase [My Copy] Journal of Medicinal Chemistry, Vol. 36 (1993), pp. 2142-2167. by Amedeo Caflisch, Andrew Miranker, Martin Karplus posted to file-import-09-01-07b by dfgreen on 2009-01-07 18:52:10 as
	Absolute binding free energies: A quantitative approach for their calculation [My Copy] Journal of Physical Chemistry B, Vol. 107 (2003), pp. 9535-9551. by Stefan Boresch, Franz Tettinger, Martin Leitgeb, Martin Karplus posted to file-import-09-01-07b by dfgreen on 2009-01-07 18:52:04 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

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