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middledomains library [187 articles]

Neue Artikel in middledomains Bibliothek.
  • Protein Folding: Complexity to Make More Complexity?. In the Pipeline:
    posted to protein folding by middledomain on 2008-10-05 12:52:32 as **
  • Evaluation of an inverse molecular design algorithm in a model binding site
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by David J Huggins, Michael D Altman, Bruce Tidor
    posted to electrostatic by middledomain on 2008-10-05 12:50:27 as ** along with 1 person and 2 groups barry structural_bioinformatics McCammon
  • Can Descriptors of the Electron Density Distribution Help To Distinguish Functional Groups?
    J. Chem. Inf. Model. (3 October 2008)
    by Julien Burton, Nathalie Meurice, Laurence Leherte, Daniel P Vercauteren
    posted to atom_type by middledomain on 2008-10-05 12:42:13 as **
  • An Interface between the Universal Force Field and the Effective Fragment Potential Method
    J. Phys. Chem. B (17 September 2008)
    by Deborah Zorn, Victor S Lin, Marek Pruski, Mark S Gordon
    posted to uff force_field eff by middledomain on 2008-09-24 19:46:43 as **
  • Peptide Folding Using Multiscale Coarse-Grained Models
    J. Phys. Chem. B (20 September 2008)
    by Ian F Thorpe, Jian Zhou, Gregory A Voth
    posted to peptide force_field coarse_grained 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
    J. Chem. Theory Comput. (18 September 2008)
    by Brian R White, Carston R Wagner, Donald G Truhlar, Elizabeth A Amin
    posted to mmff force_field comparison charge amber by middledomain on 2008-09-24 19:38:44 as **
  • On the Art of Compiling and Using 'Drug-Like' Chemical Fragment Spaces
    ChemMedChem, Vol. 9999, No. 9999. (2008), NA.
    by Jörg Degen, Christof Wegscheid-Gerlach, Andrea Zaliani, Matthias Rarey
    posted to chemical_space by middledomain on 2008-09-24 19:31:03 as ** along with 1 person zimbo1
  • Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 999A. (2008), NA.
    by Paul Labute
    posted to conformation by middledomain on 2008-09-24 19:29:47 as ** along with 2 people barry RamuAnandakrishnan
  • Using genetic algorithms to select most predictive protein features
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Andrew Kernytsky, Burkhard Rost
    posted to genetic_algorithm feature_selection by middledomain on 2008-09-24 19:28:56 as **
  • Role of Short-Range Electrostatics in Torsional Potentials
    J. Phys. Chem. A (18 September 2008)
    by Michael G Darley, Paul L Popelier
    posted to no-tag by middledomain on 2008-09-18 21:37:21 as read
  • Conformational Simulations of Aqueous Solvated α-Conotoxin GI and Its Single Disulfide Analogues Using a Polarizable Force Field Model
    J. Phys. Chem. A (13 September 2008)
    by Nan Jiang, Jing Ma
    posted to no-tag by middledomain on 2008-09-13 09:35:38 as **
  • Set of Molecular Models Based on Quantum Mechanical Ab Initio Calculations and Thermodynamic Data
    J. Phys. Chem. B (13 September 2008)
    by Bernhard Eckl, Jadran Vrabec, Hans Hasse
    posted to no-tag by middledomain on 2008-09-13 09:33:57 as **
  • Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field
    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 peptide force_field by middledomain on 2008-09-11 19:58:37 as **
  • A multipole-based water potential with implicit polarization for biomolecular simulations
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by TR Walsh, T Liang
    posted to water polarizable force_field by middledomain on 2008-09-11 19:55:41 as **
  • An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields
    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 **
  • On the Balance of Simplification and Reality in Molecular Modeling of the Electron Density
    J. Chem. Theory Comput. (10 September 2008)
    by Peter L Warburton, Jenna L Wang, Paul G Mezey
    posted to no-tag by middledomain on 2008-09-10 20:45:54 as **
  • Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Zanxia Cao, Zhixiong Lin, Jun Wang, Haiyan Liu
    posted to peptide gromos force_field conformation charge by middledomain on 2008-09-10 20:44:26 as **
  • Conformational dependence of charges in protein simulations
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Pär Söderhjelm, Ulf Ryde
    posted to protein conformation charge by middledomain on 2008-09-10 20:43:30 as **
  • A Polarizable Force Field for Computing the Infrared Spectra of the Polypeptide Backbone
    J. Phys. Chem. B (9 September 2008)
    by Verena Schultheis, Rudolf Reichold, Bernhard Schropp, Paul Tavan
    posted to polarizable peptide force_field conformation by middledomain on 2008-09-10 20:42:02 as **
  • On the treatment of long-range interactions in global potential energy surfaces for chemically bound systems
    Molecular Physics, Vol. 106, No. 9. (2008), pp. 1267-1273.
    by LL Lodi, OL Polyansky, J Tennyson
    posted to no-tag by middledomain on 2008-09-09 21:25:22 as **
  • An optimised molecular model for ammonia
    Molecular Physics, Vol. 106, No. 8. (April 2008), pp. 1039-1046.
    by Eckl, Bernhard, Vrabec, Jadran, Hasse, Hans
    posted to no-tag by middledomain on 2008-09-09 21:25:07 as **
  • The equivalent potential of water molecules for electronic structure of alanine
    Molecular Physics, Vol. 106, No. 11. (2008), pp. 1427-1439.
    by Shu Yan, Haoping Zheng, Tian Zhang
    posted to alanine by middledomain on 2008-09-09 21:23:42 as **
  • Hydration Water and Bulk Water in Proteins Have Distinct Properties in Radial Distributions Calculated from 105 Atomic Resolution Crystal Structures
    J. Phys. Chem. B (28 August 2008)
    by Xianfeng Chen, Irene Weber, Robert W Harrison
    posted to protein water by middledomain on 2008-08-29 09:52:37 as **
  • <I>Ab initio</I> calculations on halogen-bonded complexes and comparison with density functional methods
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Yun-Xiang Lu, Jian-Wei Zou, Ji-Cai Fan, Wen-Na Zhao, Yong-Jun Jiang, Qing-Sen Yu
    posted to no-tag by middledomain on 2008-08-27 15:57:57 as **
  • Application of error-ranked singular value decomposition for the determination of potential-derived atomic-centered point charges
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Jeffrey S Tan, Stephan XM Boerrigter, Raymond P Scaringe, Kenneth R Morris
    posted to no-tag by middledomain on 2008-08-27 15:56:48 as **
  • Electrostatic Properties of Aqueous Salt Solution Interfaces: A Comparison of Polarizable and Nonpolarizable Ion Models
    J. Phys. Chem. B (20 August 2008)
    by Lee G Warren, Sandeep Patel
    posted to charmm drude force_field ion polarization water by middledomain on 2008-08-20 12:00:10 as ** along with 1 person paulschlesinger
  • Toward accurate relative energy predictions of the bioactive conformation of drugs
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Keith T Butler, Javier F Luque, Xavier Barril
    posted to conformation dft by middledomain on 2008-08-19 14:56:15 as **
  • Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Wenbo Yu, Lei Liang, Zijing Lin, Sanliang Ling, Maciej Haranczyk, Maciej Gutowski
    posted to amino_acid comparison dft by middledomain on 2008-08-19 14:16:28 as **
  • Building alternate protein structures using the elastic network model
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Qingyi Yang, Kim A Sharp
    posted to no-tag by middledomain on 2008-08-17 12:51:48 as **
  • Docking and scoring with alternative side-chain conformations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Christoph Hartmann, Iris Antes, Thomas Lengauer
    posted to docking rotamers by middledomain on 2008-08-17 12:47:37 as ** along with 2 people zimbo1 reyez
  • Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Eshel Faraggi, Bin Xue, Yaoqi Zhou
    posted to neural_networks prediction solvant_accessible_surface torsion by middledomain on 2008-08-16 16:47:56 as **
  • Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Angelika Fuchs, Andreas Kirschner, Dmitrij Frishman
    posted to neural_networks prediction protein by middledomain on 2008-08-16 16:34:00 as **
  • A Linear Energy Relationship between Activation Energy and Absolute Hardness: A Case Study with the O(3P) Atom-Addition Reactions to Polyaromatic Hydrocarbons
    J. Phys. Chem. A (16 August 2008)
    by Juan F Orrego, Thanh N Truong, Fanor Mondrago&#x301;n
    posted to hardness by middledomain on 2008-08-16 15:47:25 as **
  • Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems
    Science, Vol. 321, No. 5890. (8 August 2008), pp. 798-800.
    by Michael L Klein, Wataru Shinoda
    posted to no-tag by middledomain on 2008-08-16 15:14:06 as ** along with 5 people abebe skumagai zwang pbartlett dgront
  • Insights into Current Limitations of Density Functional Theory
    Science, Vol. 321, No. 5890. (8 August 2008), pp. 792-794.
    by Aron J Cohen, Paula Mori-Sanchez, Weitao Yang
    posted to no-tag by middledomain on 2008-08-16 15:13:22 as ** along with 1 person paulschlesinger
  • Intermolecular Potentials
    Science, Vol. 321, No. 5890. (8 August 2008), pp. 787-789.
    by Anthony J Stone
    posted to no-tag by middledomain on 2008-08-16 15:12:17 as ** along with 1 person paulschlesinger
  • Theoretical Possibilities
    Science, Vol. 321, No. 5890. (8 August 2008), 783.
    by Julia Fahrenkamp-Uppenbrink, Phil Szuromi, Jake Yeston, Robert Coontz
    posted to no-tag by middledomain on 2008-08-16 15:11:37 as **
  • Are Current Molecular Dynamics Force Fields too Helical?
    Biophys. J., Vol. 95, No. 1. (1 July 2008), pp. L07-9.
    by Robert B Best, Nicolae-Viorel Buchete, Gerhard Hummer
    posted to comparison force_field md by middledomain on 2008-08-14 16:45:58 as ** along with 2 people dmobley loison
  • CHARMMing: A New, Flexible Web Portal for CHARMM
    J. Chem. Inf. Model. (13 August 2008)
    by Benjamin T Miller, Rishi P Singh, Jeffery B Klauda, Milan Hodos&#x30c;c&#x30c;ek, Bernard R Brooks, Lee H Woodcock
    posted to charmm web_interface by middledomain on 2008-08-13 13:11:15 as ** along with 2 people and 1 group jmccammon reyez McCammon
  • Accurate Molecular Polarizabilities Based on Continuum Electrostatics
    J. Chem. Theory Comput. (13 August 2008)
    by Jean-Franc&#x327;ois Truchon, Anthony Nicholls, Radu I Iftimie, Beno&#xee;t Roux, Christopher I Bayly
    posted to b3lyp polarizability by middledomain on 2008-08-13 13:09:53 as ** along with 1 person dmobley
  • Systematic Comparison of Empirical Forcefields for Molecular Dynamic Simulation of Insulin
    J. Phys. Chem. B (12 August 2008)
    by Nevena Todorova, Sue F Legge, Herbert Treutlein, Irene Yarovsky
    posted to amber charmm comparison force_field gromos by middledomain on 2008-08-12 15:09:51 as ** along with 1 person agrossfield
  • Development and Validation of AMANDA, a New Algorithm for Selecting Highly Relevant Regions in Molecular Interaction Fields
    J. Chem. Inf. Model. (12 August 2008)
    by A&#x301;ngel Dura&#x301;n, Guillermo C Marti&#x301;nez, Manuel Pastor
    posted to no-tag by middledomain on 2008-08-12 13:39:32 as **
  • Polarization of Water in the First Hydration Shell of K+ and Ca2+ Ions
    J. Phys. Chem. B (12 August 2008)
    by Denis Bucher, Serdar Kuyucak
    posted to dipole ion water by middledomain on 2008-08-12 13:37:58 as **
  • Torsional Barriers and Equilibrium Angle of Biphenyl: Reconciling Theory with Experiment
    J. Chem. Theory Comput. (8 August 2008)
    by Mikael P Johansson, Jeppe Olsen
    posted to b3lyp ccsd torsion by middledomain on 2008-08-11 14:59:06 as **
  • Beyond Point Charges: Dynamic Polarization from Neural Net Predicted Multipole Moments
    J. Chem. Theory Comput. (7 August 2008)
    by Michael G Darley, Chris M Handley, Paul L Popelier
    posted to neural_networks polarization by middledomain on 2008-08-07 10:20:18 as read
  • Comparative Study of Machine-Learning and Chemometric Tools for Analysis of In-Vivo High-Throughput Screening Data
    J. Chem. Inf. Model. (6 August 2008)
    by Kirk Simmons, John Kinney, Aaron Owens, Dan Kleier, Karen Bloch, Dave Argentar, Alicia Walsh, Ganesh Vaidyanathan
    posted to comparison hts machine_learning by middledomain on 2008-08-06 12:06:58 as ** along with 2 people jyuh zimbo1
  • Beyond the Lennard-Jones model: a simple and accurate potential function probed by high resolution scattering data useful for molecular dynamics simulations
    Phys. Chem. Chem. Phys. (2008)
    by Fernando Pirani, Simona Brizi, Luiz F Roncaratti, Piergiorgio Casavecchia, David Cappelletti, Franco Vecchiocattivi
    posted to lennard-jones md by middledomain on 2008-08-04 10:11:47 as **
  • Optimising an artificial neural network for predicting the melting point of ionic liquids
    Phys. Chem. Chem. Phys. (2008)
    by Jose S Torrecilla, Francisco Rodriguez, Jose L Bravo, Gadi Rothenberg, Kenneth R Seddon, Ignacio Lopez-Martin
    posted to neural_networks by middledomain on 2008-08-04 10:10:13 as **
  • Conformations of amino acids in proteins
    Acta Crystallographica Section D, Vol. 58, No. 5. (2002), pp. 768-776.
    posted to conformation proteins by middledomain on 2008-08-01 10:24:44 as **
  • Improved Treatment of the Protein Backbone in Empirical Force Fields
    J. Am. Chem. Soc., Vol. 126, No. 3. (28 January 2004), pp. 698-699.
    by AD Mackerell, M Feig, CL Brooks
    posted to charmm dipeptides force_field torsion by middledomain on 2008-08-01 09:31:27 as read along with 1 person hlwoodcock
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