Tag force_field [129 articles] Export

Recent papers classified by the tag force_field.

	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, 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 molecular_dynamics force_field charmm by jmparks on 2009-10-15 16:39:07 as along with 12 people dsmueller rpetrenko jrperillaj Diego_Prada oceanwind dfgreen mkrishna timg dimka ttjoseph papatonyhill ssomani
	Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling [My Copy] Journal of Computational Chemistry, Vol. 26, No. 7. (May 2005), pp. 682-690. by Eric J. Sorin, Vijay S. Pande posted to parametrization force_field by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-10-01 16:12:43 as along with 2 people allmensch GermanErlenkamp
	Solvent dramatically affects protein structure refinement [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 51. (23 December 2008), pp. 20239-20244. by Gaurav Chopra, Christopher M. Summa, Michael Levitt posted to solvent_model refinement potencial force_field energy_minimization by rabio on 2009-09-29 14:05:09 as along with 7 people and 4 groups pavanghatty mijam dgront barry sobolevnrm biehl itmeson structural_bioinformatics McCammon Bioinformatics baker-group
	A force field for virtual atom molecular mechanics of proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15667-15672. by Anil Korkut, Wayne A. Hendrickson posted to nma force_field coarse_grain by barry to the group structural_bioinformatics on 2009-09-28 19:29:39 as along with 1 person and 1 group jmccammon McCammon
	CREDO: A Protein-Ligand Interaction Database for Drug Discovery [My Copy] Chemical Biology & Drug Design, Vol. 73, No. 2. (February 2009), pp. 157-167. by Adrian Schreyer, Tom Blundell posted to ligands force_field docking by mijam on 2009-09-28 13:07:30 as along with 6 people richardbickerton pansapiens bicko nanonan massivemayhem higueruelo
	MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries [My Copy] Journal of Computational Chemistry, Vol. 20, No. 7. (1999), pp. 730-748. by Thomas A. Halgren posted to force_field by mijam on 2009-09-24 18:28:30 as
	Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Zhongqiao Hu, Jianwen Jiang posted to force_field by RamuAnandakrishnan on 2009-05-29 14:41:37 as
	Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Minoru Saito, Isao Okazaki posted to force_field parameterization by middledomain on 2009-05-06 19:25:31 as
	Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Claudio A. Morgado, Petr Jurečka, Daniel Svozil, Pavel Hobza, Jiří Šponer posted to comparison force_field stacking by middledomain on 2009-05-06 18:35:26 as along with 1 person Romaniz
	Transferable Coarse-Grained Models for Ionic Liquids [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (14 April 2009), pp. 1091-1098. by Yanting Wang, Shulu Feng, Gregory A. Voth posted to coarse_grained force_field parametrization solvent by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-04-22 11:43:54 as
	Evaluation of Density Functionals and Basis Sets for Carbohydrates [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (14 April 2009), pp. 679-692. by Gábor I. Csonka, Alfred D. French, Glenn P. Johnson, Carlos A. Stortz posted to dft force_field parametrization resp by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-04-22 10:58:14 as along with 2 people Fortran carlosjavierna
	Unorthodox uses of Bennett's acceptance ratio method [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Gerhard König, Stefan Bruckner, Stefan Boresch posted to force_field implicit_solvent by RamuAnandakrishnan on 2009-04-17 13:20:58 as along with 2 people ssomani agrossfield
	High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Hideaki Fujitani, Azuma Matsuura, Sino Sakai, Hiroyuki Sato, Yoshiaki Tanida posted to force_field by middledomain on 2009-04-12 14:42:29 as along with 2 people carlosjavierna Fortran
	Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 4. (27 April 2009), pp. 944-955. by Robert S. Paton, Jonathan M. Goodman posted to comparison force_field hydrogen_bonding by middledomain on 2009-04-12 14:38:02 as along with 2 people massivemayhem carlosjavierna
	A multipole-based water potential with implicit polarization for biomolecular simulations [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by T. R. Walsh, T. Liang posted to force_field parametrization protein water by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-03-16 10:48:38 as along with 1 person middledomain
	Assessment of standard force field models against high-quality <I>ab initio</I> potential curves for prototypes of pi-pi, CH/pi, and SH/pi interactions [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2187-2193. by C. David Sherrill, Bobby G. Sumpter, Mutasem O. Sinnokrot, et al.Michael S. Marshall, Edward G. Hohenstein, Ross C. Walker, Ian R. Gould posted to force_field by RamuAnandakrishnan on 2009-02-26 16:49:16 as along with 1 person and 1 group oteri Structural Biology Group TorVergata
	Molecular Modeling of Complex Chemical Systems [My Copy] Journal of the American Chemical Society, Vol. 130, No. 50. (17 December 2008), pp. 16824-16827. by Donald G. Truhlar posted to docking force_field by middledomain on 2009-02-23 11:56:02 as along with 1 person flbarroso
	Molecular Mechanics Force Field for Octahedral Organometallic Compounds with Inclusion of the Trans Influence [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Ivan Tubert-Brohman, Maurus Schmid, Markus Meuwly posted to force_field valbond by middledomain on 2009-02-23 11:46:08 as
	Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Cezary Czaplewski, Sebastian Kalinowski, Adam Liwo, Harold A. Scheraga posted to force_field protein unres by middledomain on 2009-02-23 11:43:36 as
	X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 3. (10 March 2009), pp. 459-467. by Wangshen Xie, Modesto Orozco, Donald G. Truhlar, Jiali Gao posted to electrosatics force_field md xpol by middledomain on 2009-02-23 11:16:05 as
	Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 3. (10 March 2009), pp. 615-626. by Andreas Kukol posted to all_atom force_field gromos lipid membrane by middledomain on 2009-02-23 11:12:30 as along with 3 people and 1 group arnaucordomi dimka Marine Molecular dynamics in MSU
	GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by F. Iori, R. Di Felice, E. Molinari, S. Corni posted to ab-initio force_field parametrization protein surface by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-02-06 13:45:21 as
	The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Michio Iwaoka, Naoki Kimura, Daisuke Yosida, Toshiya Minezaki posted to force_field protein saap by middledomain on 2009-02-01 13:11:51 as
	MM3(96) parameterization for camptothecin analogs: An ab initio and molecular mechanics study [My Copy] Journal of Computer-Aided Molecular Design, Vol. 11, No. 1. (1 January 1997), pp. 61-70. by Sean W. Carrigan, Jenn-Huei Lii, Phillip J. Bowen posted to camptothecin force_field parametrization by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-01-15 16:22:58 as
	Application of the RESP Methodology in the Parametrization of Organic Solvents [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 41. (1 October 1998), pp. 8070-8079. by Thomas Fox, Peter A. Kollman posted to force_field parametrization resp by A_Coletta_Thesis on 2009-01-15 15:09:56 as along with 1 person and 1 group mikaellund Structural Biology Group TorVergata
	An <I>ab initio</I> force field for the cofactors of bacterial photosynthesis [My Copy] Journal of Computational Chemistry, Vol. 24, No. 2. (2003), pp. 129-142. by Matteo Ceccarelli, Piero Procacci, Massimo Marchi posted to ab-initio dft force_field parametrization by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-01-15 10:32:15 as
	Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters [My Copy] Journal of Computer-Aided Molecular Design, Vol. 20, No. 1. (January 2006), pp. 13-25. by Curco, David, Rodriguez-Ropero, Francisco, Aleman, Carlos posted to ab-initio dft force_field molecular_dynamics parametrization by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-01-15 10:28:20 as along with 1 person AndreaColetta
	Development and initial testing of an empirical forcefield for simulation of poly(alkylthiophenes) [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 1. (August 2008), pp. 34-44. by A. Widge, Y. Matsuoka, M. Kurnikova posted to force_field molecular_dynamics parametrization by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-01-14 18:07:59 as
	Derivation of Force Fields for Molecular Mechanics and Dynamics from ab initio Energy Surfaces [My Copy] Proceedings of the National Academy of Sciences, Vol. 85, No. 15. (1 August 1988), pp. 5350-5354. by Jon R. Maple, Uri Dinur, Arnold T. Hagler posted to ab-initio force_field parametrization by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-01-14 17:10:46 as
	Automatic parameterization of force field by systematic search and genetic algorithms [My Copy] Journal of Computational Chemistry, Vol. 22, No. 12. (2001), pp. 1219-1228. by Junmei Wang, Peter A. Kollman posted to ab-initio force_field molecular_dynamics parametrization by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-01-14 17:06:24 as along with 1 person RamuAnandakrishnan
	The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 27. (1 July 2007), pp. 7812-7824. by Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, Alex H. de Vries posted to coarse_grained force_field molecular_dynamics parametrization by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-01-14 16:37:44 as along with 7 people and 1 group anuragsethi sunrise Marine choonpeng softsimu dimka sunnytov Molecular dynamics in MSU
	GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447. by Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl posted to force_field molecular_dynamics parametrization by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-01-14 16:32:25 as along with 22 people and 1 group softsimu parnell rabio oteri krapnik robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm r2s2 middledomain loison baker-group
	The MARTINI Coarse-Grained Force Field: Extension to Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 5. (1 May 2008), pp. 819-834. by Luca Monticelli, Senthil K. Kandasamy, Xavier Periole, Ronald G. Larson, D. Peter Tieleman, Siewert-Jan Marrink posted to coarse_grained force_field molecular_dynamics parametrization by A_Coletta_Thesis on 2009-01-14 16:31:31 as along with 13 people and 3 groups arnaucordomi dimka oteri sunrise flbarroso krapnik Marine middledomain sobolevnrm Ema aqeel DanielParton softsimu Structural Biology Group TorVergata Molecular dynamics in MSU baker-group
	Continuum polarizable force field within the Poisson-Boltzmann framework. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 25. (26 June 2008), pp. 7675-7688. by Y. H. Tan, C. Tan, J. Wang, R. Luo posted to force_field by RamuAnandakrishnan on 2008-12-24 23:21:11 as along with 1 person onufriev
	Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Lennart Nilsson posted to charmm force_field by middledomain on 2008-12-20 16:02:58 as along with 1 person RamuAnandakrishnan
	Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. [My Copy] Journal of computational chemistry, Vol. 30, No. 12. (September 2009), pp. 1821-1838. by P. E. Lopes, G. Lamoureux, A. D. Mackerell posted to charmm drude force_field polarizable by middledomain on 2008-12-20 15:22:45 as along with 1 person flbarroso
	Knowledge-based potentials in protein design [My Copy] Current Opinion in Structural Biology In Membranes / Engineering and design, Vol. 16, No. 4. (August 2006), pp. 508-513. by Alan M. Poole, Rama Ranganathan posted to cabs comparative_modeling force_field interaction_hierarchy intro knowledge_based_potentials lattice_model lattice_models modeling mqap prediction protein protein_folding protein_structure review structure strutcture_prediction by mcbla on 2008-11-24 00:25:28 as along with 5 people and 2 groups flbarroso nigham marcius rabio bethbromley BioinfoCIPF SGU-CIPF
	The Important Role of Lone-Pairs in Force Field (MM4) Calculations on Hydrogen Bonding in Alcohols [My Copy] The Journal of Physical Chemistry A, Vol. 112, No. 46. (20 November 2008), pp. 11903-11913. by Jenn-Huei Lii, Norman L. Allinger posted to force_field hydrogen_bonding mm4 by middledomain on 2008-11-02 11:35:33 as
	Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 11. (11 November 2008), pp. 1891-1901. by Wei Han, Cheuk-Kin Wan, Yun-Dong Wu posted to force_field torsion by middledomain on 2008-10-19 17:07:49 as along with 3 people sunrise rbaron agrossfield
	An Interface between the Universal Force Field and the Effective Fragment Potential Method [My Copy] J. Phys. Chem. B (17 September 2008) by Deborah Zorn, Victor S. Lin, Marek Pruski, Mark S. Gordon posted to eff force_field uff by middledomain on 2008-09-24 19:46:43 as
	Peptide Folding Using Multiscale Coarse-Grained Models [My Copy] J. Phys. Chem. B (20 September 2008) by Ian F. Thorpe, Jian Zhou, Gregory A. Voth posted to coarse_grained force_field peptide by middledomain on 2008-09-24 19:44:45 as along with 3 people agrossfield A_Coletta_Thesis paulschlesinger
	Molecular Modeling of Geometries, Charge Distributions, and Binding Energies of Small, Druglike Molecules Containing Nitrogen Heterocycles and Exocyclic Amino Groups in the Gas Phase and in Aqueous Solution [My Copy] J. Chem. Theory Comput. (18 September 2008) by Brian R. White, Carston R. Wagner, Donald G. Truhlar, Elizabeth A. Amin posted to amber charge comparison force_field mmff by middledomain on 2008-09-24 19:38:44 as
	Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Amanda M. Salisburg, Ashley L. Deline, Katrina W. Lexa, George C. Shields, Karl N. Kirschner posted to force_field peptide by middledomain on 2008-09-11 19:58:37 as
	An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 999A. (2008), NA. by Paul C. Whitford, Jeffrey K. Noel, Shachi Gosavi, Alexander Schug, Kevin Y. Sanbonmatsu, José N. Onuchic posted to force_field by middledomain on 2008-09-10 20:56:52 as along with 1 person flbarroso
	Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field [My Copy] Journal of Computational Chemistry, Vol. 30, No. 4. (2009), pp. 645-660. by Zanxia Cao, Zhixiong Lin, Jun Wang, Haiyan Liu posted to charge conformation force_field gromos peptide by middledomain on 2008-09-10 20:44:26 as
	A Polarizable Force Field for Computing the Infrared Spectra of the Polypeptide Backbone [My Copy] J. Phys. Chem. B (9 September 2008) by Verena Schultheis, Rudolf Reichold, Bernhard Schropp, Paul Tavan posted to conformation force_field peptide polarizable by middledomain on 2008-09-10 20:42:02 as
	A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations [My Copy] Journal of Computational Chemistry, Vol. 24, No. 16. (December 2003), pp. 1999-2012. by Yong Duan, Chun Wu, Shibasish Chowdhury, et al.Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, James Caldwell, Junmei Wang, Peter Kollman posted to force_field molecular_dynamics resp by A_Coletta_Thesis on 2008-09-09 12:02:16 as along with 6 people and 1 group Vadikus flbarroso ashaytan Lombardo_7 xdeupi schlauchi LabCompMed
	Phi/psi-chology: Ramachandran revisited. [My Copy] Structure, Vol. 4, No. 12. (15 December 1996), pp. 1395-1400. by G. J. Kleywegt, T. A. Jones posted to force_field protein_structure by dgront on 2008-09-08 17:29:18 as along with 3 people krapnik aqeel xiaobeizhao
	Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 72, No. 1. (2008), pp. 62-73. by El-Ad D. Amir, Nir Kalisman, Chen Keasar posted to force_field by dgront on 2008-08-29 19:07:19 as along with 2 people rsantana mijam
	Comparison of simple potential functions for simulating liquid water [My Copy] The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935. by William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein posted to force_field by RamuAnandakrishnan on 2008-08-22 23:29:06 as along with 17 people and 1 group jmparks fralium bmduggan kulinskii ibuch Lombardo_7 paddydu dfgreen softsimu mleis ttjoseph ffranca easybakemuffin ashaytan r2s2 pavanghatty Diego_Prada CMB

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parametrization	28
molecular_dynamics	17
charmm	13
amber	12
md	12
ab-initio	10
protein	10
review	8
coarse_grained	7
dft	7
polarization	7
comparison	6
peptide	5
potential	5
water	5
comparative_modeling	4
mqap	4
resp	4
charge	3
coarse_grain	3
conformation	3
gromos	3
implicit_solvation	3
mmff	3
nma	3
parameterization	3
polarizable	3
protein_folding	3
protein_structure	3
torsion	3
camptothecin	2
dce	2
dipeptides	2
docking	2
drude	2
electrosatics	2
energy	2
hydrogen_bonding	2
interaction_hierarchy	2
intro	2
knowledge_based_potentials	2
ligand	2
mm3	2
nucleic_acids	2
opls	2
phd	2
refinement	2
rehabilitation_robotics	2
solvent	2
surface	2
trappe	2
unres	2
xpol	2
alcohol	1
ameoba	1
amino_acid	1
ann	1
atomic_charges	1
bayesian	1
benzene	1
cabs	1
charge_on_spring_model	1
coarse-grained	1
compass	1
continuous_models	1
eff	1
efp	1
electrostatics	1
energy_minimization	1
glassy_polymer	1
gromacs	1
gui	1
industry	1
ion	1
kremer	1
lattice_models	1
ligands	1
lipid	1
mean-field	1
mm2	1
modeling	1
molecular_interaction	1
monte_carlo	1
multipole_expansion	1
my_own	1
pi-pi_interactions	1
polycarbonate	1
q2mm	1
qsar	1
ramachandran	1
reduced_models	1
saap	1
simulation	1
simulation_methods	1
solvation	1
solvent_model	1
strain_hardening	1
structure_prediction	1
strutcture_prediction	1
web_interface	1

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