Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?
出版年份 2018 全文链接
标题
Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?
作者
关键词
Force fields: force field derivation, Potential functions, van der Waals, Hydrogen bond: drug discovery, Molecular dynamics, Molecular mechanics, Protein simulation, Molecular simulation, Nonbond interactions, Combination rules, Polarizability, Charge flux, Nonbond flux, Polarizability flux, Free energy, Coupling terms, Cross terms, AMBER, Charmm, OPLS, GAFF, AMOEBA, SDFF, CFF, VFF, Consistent force field, Electrostatics, Multipole moments, Quantum derivative fitting, QDF
出版物
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume -, Issue -, Pages -
出版商
Springer Nature
发表日期
2018-11-30
DOI
10.1007/s10822-018-0111-4
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics
- (2018) A. T. Hagler JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions
- (2016) Gerardo Andrés Cisneros et al. CHEMICAL REVIEWS
- Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model
- (2016) Karl T. Debiec et al. Journal of Chemical Theory and Computation
- CHARMM36m: an improved force field for folded and intrinsically disordered proteins
- (2016) Jing Huang et al. NATURE METHODS
- Quantum Derivative Fitting and Biomolecular Force Fields: Functional Form, Coupling Terms, Charge Flux, Nonbond Anharmonicity, and Individual Dihedral Potentials
- (2015) A. T. Hagler Journal of Chemical Theory and Computation
- Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment
- (2015) Sarah Rauscher et al. Journal of Chemical Theory and Computation
- Molecular dynamics simulations on scattering of single Ar, N2, and CO2 molecules on realistic surfaces
- (2014) J. Reinhold et al. COMPUTERS & FLUIDS
- Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. III. Impact of combining rules on mixtures properties
- (2014) Caroline Desgranges et al. JOURNAL OF CHEMICAL PHYSICS
- Perspective: Fifty years of density-functional theory in chemical physics
- (2014) Axel D. Becke JOURNAL OF CHEMICAL PHYSICS
- Advanced Potential Energy Surfaces for Condensed Phase Simulation
- (2013) Omar Demerdash et al. Annual Review of Physical Chemistry
- Conformational Polymorphism
- (2013) Aurora J. Cruz-Cabeza et al. CHEMICAL REVIEWS
- Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences
- (2013) Art D. Bochevarov et al. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
- Charge mobility in molecules: Charge fluxes from second derivatives of the molecular dipole
- (2013) Daria Galimberti et al. JOURNAL OF CHEMICAL PHYSICS
- Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins
- (2013) Yue Shi et al. Journal of Chemical Theory and Computation
- On the Anisotropy of van der Waals Atomic Radii of O, S, Se, F, Cl, Br, and I
- (2013) Hamed Eramian et al. JOURNAL OF PHYSICAL CHEMISTRY A
- Systematic Improvement of a Classical Molecular Model of Water
- (2013) Lee-Ping Wang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- ZINC: A Free Tool to Discover Chemistry for Biology
- (2012) John J. Irwin et al. Journal of Chemical Information and Modeling
- Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol
- (2012) Bruno A. C. Horta et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- The errors of our ways: taking account of error in computer-aided drug design to build confidence intervals for our next 25 years
- (2012) Terry Richard Stouch JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test
- (2011) David A. Bardwell et al. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE
- Definition and testing of the GROMOS force-field versions 54A7 and 54B7
- (2011) Nathan Schmid et al. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
- Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules
- (2011) Pengyu Ren et al. Journal of Chemical Theory and Computation
- New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters
- (2011) Bruno A. C. Horta et al. Journal of Chemical Theory and Computation
- Understanding molecular structure from molecular mechanics
- (2011) Norman L. Allinger JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Simulating water with rigid non-polarizable models: a general perspective
- (2011) Carlos Vega et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Quantum Mechanical Methods for Drug Design
- (2010) Ting Zhou et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
- Properties of liquid water from a systematic refinement of a high-rank multipolar electrostatic potential
- (2010) Majeed S. Shaik et al. JOURNAL OF CHEMICAL PHYSICS
- Hydrogen bonded network properties in liquid formamide
- (2010) Imre Bakó et al. JOURNAL OF CHEMICAL PHYSICS
- The structure of ambient water
- (2010) Gary N.I. Clark et al. MOLECULAR PHYSICS
- Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials
- (2010) Sarah L. Price et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- How molecules stick together in organic crystals: weak intermolecular interactions
- (2009) Jack D. Dunitz et al. CHEMICAL SOCIETY REVIEWS
- Properties of water along the liquid-vapor coexistence curve via molecular dynamics simulations using the polarizable TIP4P-QDP-LJ water model
- (2009) Brad A. Bauer et al. JOURNAL OF CHEMICAL PHYSICS
- Incorporating Phase-Dependent Polarizability in Nonadditive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid−Vapor Interface
- (2009) Brad A. Bauer et al. Journal of Chemical Theory and Computation
- Molecular dynamics simulations of AP/HMX composite with a modified force field
- (2009) Wei Zhu et al. JOURNAL OF HAZARDOUS MATERIALS
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