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	AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules [My Copy] Computer Physics Communications, Vol. 91, No. 1-3. (02 September 1995), pp. 1-41. by D Pearlman, posted to force-field by rdf on 2009-12-10 13:34:39 as along with 3 people abovell papatonyhill gruppo
	UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations [My Copy] Journal of the American Chemical Society In Journal of the American Chemical Society, Vol. 114, No. 25. (1 December 1992), pp. 10024-10035. by A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard, W. M. Skiff posted to uff force-field by rdf on 2009-12-03 15:24:39 as along with 2 people egonw flbarroso
	Interaction Model for the Adsorption of Organic Molecules on the Silver Surface [My Copy] In The Journal of Physical Chemistry B, Vol. 110, No. 11. (1 March 2006), pp. 5595-5601. by Jukka-Pekka Jalkanen, Francesco Zerbetto posted to silver organic force-field by rdf on 2009-12-03 14:17:17 as
	The COMPASS force field: parameterization and validation for phosphazenes [My Copy] Computational and Theoretical Polymer Science, Vol. 8, No. 1-2. (1998), pp. 229-246. by H Sun, posted to force-field by rdf on 2009-12-03 12:51:14 as
	SHAPES empirical force field: new treatment of angular potentials and its application to square-planar transition-metal complexes [My Copy] In Journal of the American Chemical Society, Vol. 113, No. 1. (1 January 1991), pp. 1-12. by Viloya S. Allured, Christine M. Kelly, Clark R. Landis posted to force-field angular by rdf on 2009-12-03 12:37:19 as
	Empirical force fields for biological macromolecules: overview and issues. [My Copy] Journal of computational chemistry, Vol. 25, No. 13. (1 October 2004), pp. 1584-1604. by A. D. Mackerell posted to force-field by krapnik on 2009-12-01 14:23:49 as along with 8 people and 3 groups flbarroso whitead BragilMassoud marcius dgront loison mirzazadeh AndreaColetta Jiang Research Group BioinfoCIPF SGU-CIPF
	Inorganic and bioinorganic molecular mechanics modeling—the problem of the force field parameterization [My Copy] Coordination Chemistry Reviews, Vol. 238-239 (March 2003), pp. 9-20. by P. Comba posted to potential parametrization force-field by rdf on 2009-12-01 14:00:11 as
	Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective† [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 43. (29 October 2009), pp. 11938-11948. by De, Ross C. Walker, Adrian E. Roitberg posted to semiempirical molecular modeling force-field by zfekete on 2009-11-03 09:59:16 as along with 2 people jjurban carlosjavierna
	Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids [My Copy] Journal of the American Chemical Society In Journal of the American Chemical Society, Vol. 118, No. 45. (1 January 1996), pp. 11225-11236. by William L. Jorgensen, David S. Maxwell, Julian Tirado-Rives posted to opls force-field by dimka on 2009-10-29 22:31:50 as along with 11 people rabio krapnik snichols15 flbarroso tovrstra dfgreen sunnytov BragilMassoud loison softsimu Diego_Prada
	Atomistic molecular dynamics study of interface formation: Al on poly(p-phenylene vinylene) [My Copy] Physical Review B (Condensed Matter and Materials Physics), Vol. 78, No. 15. (2008), 155312. by Ronaldo Giro, Mar'ilia J. Caldas posted to uff polymer force-field aluminum by rdf on 2009-09-28 13:21:51 as
	A semiempirical free energy force field with charge-based desolvation [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (1 February 2007), pp. 1145-1152. by Ruth Huey, Garrett M. Morris, Arthur J. Olson, David S. Goodsell posted to p2 force-field by nickolay on 2009-09-10 15:29:08 as along with 6 people and 1 group trishul joule oteri IrinaMoreira BragilMassoud carlescorbi Structural Biology Group TorVergata
	Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects [My Copy] Journal of Computational Chemistry, Vol. 23, No. 1. (2002), pp. 128-137. by Walter Rocchia, Sundaram Sridharan, Anthony Nicholls, Emil Alexov, Alessandro Chiabrera, Barry Honig posted to p2 force-field by nickolay on 2009-09-09 23:54:23 as
	Modeling of polyvinylpyrrolidone and polyvinylimidazole in aqueous solution [My Copy] Macromolecular Theory and Simulations, Vol. 7, No. 6. (1998), pp. 567-577. by Thomas Flebbe, Reinhard Hentschke, Erich Hädicke, Christian Schade posted to polyol force-field by rdf on 2009-09-08 11:18:35 as
	A Bayesian statistics approach to multiscale coarse graining [My Copy] The Journal of Chemical Physics, Vol. 129, No. 21. (2008), 214114. by Pu Liu, Qiang Shi, Hal Daumé, Gregory A. Voth posted to time thermodynamics systems space physical multi-scale modelling large-scale force-field coarse-grained chemical bayesian atom by bertelsen on 2009-09-04 20:07:28 as along with 1 person tomweingarten
	Swimming with and against the Stream: Does Motor Adaptation to Lateral Forces Influence Visual Motion Perception? [My Copy] J. Neurosci., Vol. 27, No. 49. (5 December 2007), pp. 13367-13368. by Gerrit W. Maus posted to visuospatial_experience visuomotor review motor_learning jpr200909 hand_movements force-field experience by ybysk on 2009-08-27 02:38:45 as
	All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data [My Copy] Journal of Computational Chemistry, Vol. 21, No. 2. (2000), pp. 86-104. by Nicolas Foloppe, Alexander D. Mackerell, Jr posted to charmm charmm27 force-field lipid md by dimka on 2009-07-27 20:26:34 as along with 3 people rpetrenko mkrishna easybakemuffin
	Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 35. (1 September 2006), pp. 17616-17626. by Berk Hess, Nico F. A. van der Vegt posted to force-field water by krapnik on 2009-07-27 11:36:06 as along with 6 people and 1 group softsimu arnaucordomi flbarroso Diego_Prada Marine ashaytan Molecular dynamics in MSU
	Potential energy functions for atomic-level simulations of water and organic and biomolecular systems [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6665-6670. by William L. Jorgensen, Julian Tirado-Rives posted to force-field potential water by krapnik on 2009-07-27 11:33:11 as along with 3 people r2s2 flbarroso choonpeng
	Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 9004-9015. by Robert B. Best, Gerhard Hummer posted to coil force-field force-fields helix hummer molecular-dynamics polypeptides by carlosjavierna on 2009-07-13 06:02:42 as
	Molecular mechanics and molecular dynamics study on azurin using extensible and systematic force field (ESFF) [My Copy] Journal of Molecular Structure: THEOCHEM, Vol. 907, No. 1-3. (15 August 2009), pp. 1-8. by V. Rajapandian, Sundar S. Raman, V. Hakkim, R. Parthasarathi, V. Subramanian posted to force-field force-fields by carlosjavierna on 2009-07-07 03:43:52 as
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. Brooks, C. L. Brooks, A. D. Mackerell, et al.L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus posted to force-field simulation by medic0747 on 2009-06-17 14:36:53 as along with 10 people and 1 group ckmyo dgront rodrigofaccioli mmuecke flbarroso jrperillaj xavierprat saravan sobolevnrm dimka baker-group
	The GROMOS software for biomolecular simulation: GROMOS05 [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (2005), pp. 1719-1751. by Markus Christen, Philippe H. Hünenberger, Dirk Bakowies, et al.Riccardo Baron, Roland Bürgi, Daan P. Geerke, Tim N. Heinz, Mika A. Kastenholz, Vincent Kräutler, Chris Oostenbrink, Christine Peter, Daniel Trzesniak, Wilfred F. van Gunsteren posted to force-field simulation by medic0747 on 2009-06-17 14:33:51 as
	Dominant forces in protein folding [My Copy] Biochemistry, Vol. 29, No. 31. (1 August 1990), pp. 7133-7155. by Ken A. Dill posted to folding force-field protein review by chiufanlee on 2009-04-26 23:39:51 as along with 3 people krapnik flbarroso mlg
	Comparative study of generalized Born models: protein dynamics. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6760-6764. by H. Fan, A. E. Mark, J. Zhu, B. Honig posted to dielectric_constant force-field solvatation validation by krapnik on 2009-04-07 14:07:06 as along with 1 person ttjoseph
	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 force-field protein-ligand by massivemayhem on 2009-04-01 15:10:24 as along with 2 people middledomain carlosjavierna
	Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (2009), pp. 982-992. by Karel Berka, Roman Laskowski, Kevin E. Riley, Pavel Hobza, Jiří Vondrášek posted to amber force-field function interactions potential protein quantum_chemical residue-residue side-chain validation by krapnik on 2009-03-05 11:02:22 as along with 1 person carlosjavierna
	Development of Novel Statistical Potentials Describing Cation−π Interactions in Proteins and Comparison with Semiempirical and Quantum Chemistry Approaches [My Copy] Journal of Chemical Information and Modeling, Vol. 46, No. 2. (1 March 2006), pp. 884-893. by Dimitri Gilis, Christophe Biot, Eric Buisine, Yves Dehouck, Marianne Rooman posted to force-field quantum_chemical statistical_potential validation by krapnik on 2009-02-22 12:53:51 as
	Using quantum mechanics to improve estimates of amino acid side chain rotamer energies [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 4. (2008), pp. 1637-1646. by Douglas P. Renfrew, Glenn L. Butterfoss, Brian Kuhlman posted to conformation dft force-field hf mp2 quantum_chemical side-chain validation by krapnik on 2009-02-21 18:32:09 as along with 1 person Lombardo_7
	Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 5. (2 March 1999), pp. 2025-2030. by Jooyoung Lee, Adam Liwo, Harold A. Scheraga posted to coarse-graining conformation folding force-field potential protein residue-residue simulation united-residue by krapnik on 2009-02-21 15:25:23 as along with 1 person newton1234
	A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data [My Copy] Journal of Computational Chemistry, Vol. 18, No. 7. (1997), pp. 849-873. by A. Liwo, S. O&lstrok;dziej, M. R. Pincus, R. J. Wawak, S. Rackovsky, H. A. Scheraga posted to force-field protein simulation united-atom by krapnik on 2009-02-21 15:21:35 as along with 1 person dgront
	Comparison of database potentials and molecular mechanics force fields [My Copy] Current Opinion in Structural Biology, Vol. 7, No. 2. (April 1997), pp. 194-199. by J. Moult posted to analysis force-field protein residue-residue statistical_potential validation by krapnik on 2009-02-21 11:48:45 as
	Protein Folding Simulations: Combining Coarse-grained Models and All-atom Molecular Dynamics [My Copy] Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 116, No. 1. (2006), pp. 75-86. by Giorgio Colombo, Cristian Micheletti posted to coarse-graining folding force-field potential protein by krapnik on 2009-02-20 17:21:10 as
	Coarse-graining the Self-assembly of β-helical Protein Building Blocks [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 50. (1 December 2007), pp. 14006-14011. by David Curco, Ruth Nussinov, Carlos Aleman posted to amber coarse-graining force-field potential by krapnik on 2009-02-20 12:57:39 as
	Force Field for Molecular Dynamics Studies of Glycine/Water Mixtures in Crystal/Solution Environments [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 3. (22 January 2009), pp. 752-758. by Sivashangari Gnanasambandam, Zhongqiao Hu, Jianwen Jiang, Raj Rajagopalan posted to ff force-field gly glycine md molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-20 03:20:35 as
	Biomolecular simulations of membranes: Physical properties from different force fields [My Copy] The Journal of Chemical Physics, Vol. 128, No. 12. (2008) by Shirley W. I. Siu, Robert Vácha, Pavel Jungwirth, Rainer A. Böckmann posted to force-field membrane validation by krapnik on 2009-02-07 10:57:41 as along with 4 people and 1 group robertvacha sobolevnrm paulschlesinger sunhwan baker-group
	New-Generation Amber United-Atom Force Field [My Copy] J. Phys. Chem. B, Vol. 110, No. 26. (6 July 2006), pp. 13166-13176. by L. Yang, C. Tan, M. J. Hsieh, et al.J. Wang, Y. Duan, P. Cieplak, J. Caldwell, P. A. Kollman, R. Luo posted to coarse-graining force-field modeling protein united-atom by krapnik on 2008-12-09 11:10:08 as along with 1 person ttjoseph
	Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations. [My Copy] Biophys J, Vol. 88, No. 4. (April 2005), pp. 2472-2493. by E. J. Sorin, V. S. Pande posted to folding force-field modeling potential ramachandran validation by krapnik on 2008-12-09 11:09:19 as along with 4 people paulymer ttjoseph allmensch loison
	Protein model refinement using an optimized physics-based all-atom force field [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 24. (17 June 2008), pp. 8268-8273. by Anna Jagielska, Liliana Wroblewska, Jeffrey Skolnick posted to conformation force-field interactions potential protein by krapnik on 2008-12-09 10:58:47 as along with 4 people and 2 groups RamuAnandakrishnan jmccammon barry zwang structural_bioinformatics McCammon
	Motor force field learning influences visual processing of target motion. [My Copy] J Neurosci, Vol. 27, No. 37. (12 September 2007), pp. 9975-9983. by L. E. Brown, E. T. Wilson, M. A. Goodale, P. L. Gribble posted to visuomotor visualmotor-interactions robotic motor_learning manipulandum jpr200909 force-field by ybysk on 2008-12-02 04:03:04 as along with 1 person and 1 group jillhuang VisionLab
	All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution [My Copy] Journal of Computational Chemistry, Vol. 21, No. 2. (2000), pp. 105-120. by Alexander D. Mackerell, Nilesh K. Banavali posted to charmm27-nucleicacid force-field mackerell by mkrishna on 2008-11-22 21:07:19 as along with 3 people rpetrenko gjuggler softsimu
	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 charmm22 force-field mackerell by mkrishna on 2008-11-22 21:03:23 as along with 12 people jmparks dsmueller rpetrenko jrperillaj Diego_Prada oceanwind dfgreen timg dimka ttjoseph papatonyhill ssomani
	Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 25, No. 11. (2004), pp. 1400-1415. by Alexander D. Mackerell, Michael Feig, Charles L. Brooks posted to charmm22 force-field mackerell by mkrishna on 2008-11-22 21:00:34 as along with 4 people tovrstra dgront hlwoodcock middledomain
	Examining the Contributions of Lipid Shape and Headgroup Charge on Bilayer Behavior [My Copy] Biophys. J. (30 May 2008), biophysj.107.128074. by Allison N. Dickey, Roland Faller posted to diffusion-ions electrostatics-membranes force-field by softsimu on 2008-10-02 08:20:08 as along with 3 people loison paulschlesinger agrossfield
	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 martini protein simulation by Marine to the group Molecular dynamics in MSU on 2008-09-22 10:01:59 as along with 14 people and 2 groups loison arnaucordomi dimka oteri sunrise flbarroso A_Coletta_Thesis krapnik middledomain sobolevnrm Ema aqeel DanielParton softsimu Structural Biology Group TorVergata baker-group
	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-grain force-field md simulations by dimka on 2008-05-13 21:10:45 as along with 8 people and 2 groups loison anuragsethi sunrise A_Coletta_Thesis Marine choonpeng softsimu sunnytov Structural Biology Group TorVergata Molecular dynamics in MSU
	The FoldX web server: an online force field. [My Copy] Nucleic acids research, Vol. 33, No. Web Server issue. (1 July 2005) by J. Schymkowitz, J. Borg, F. Stricher, R. Nys, F. Rousseau, L. Serrano posted to analysis foldx force-field structure webserver by neils on 2008-04-16 02:40:51 as along with 3 people GermanErlenkamp aalibes chad_davis
	Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments [My Copy] European Biophysics Journal In European Biophysics Journal, Vol. 36, No. 8. (1 November 2007), pp. 919-931. by Louic Vermeer, Bert de Groot, Valérie Réat, Alain Milon, Jerzy Czaplicki posted to double-bond force-field nmr by softsimu on 2008-04-11 19:26:50 as along with 3 people loison scampos dimka
	Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95 [My Copy] Journal of Computational Chemistry, Vol. 21, No. 9. (2000), pp. 748-762. by Satoshi Ono, Nobuyuki Nakajima, Junichi Higo, Haruki Nakamura posted to amber force-field peptides by softsimu on 2008-04-03 22:17:27 as
	Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue? [My Copy] J. Chem. Theory Comput., Vol. 3, No. 5. (11 September 2007), pp. 1851-1859. by P. Auffinger, T. E. Cheatham, A. C. Vaiana posted to force-field ions by softsimu on 2008-01-24 15:31:30 as along with 1 person robertvacha
	Hydrogen Bonding and Binding of Polybasic Residues with Negatively Charged Mixed Lipid Monolayers. [My Copy] Langmuir (23 January 2008) by Christian D. Lorenz, Jordi Faraudo, Alex Travesset posted to charmm dopc dops force-field lipid md membrane pip2 simulations by dimka on 2008-01-24 14:42:43 as along with 1 person priyaps

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