相关参考文献
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 and simulations of intrinsically disordered proteins
Jing Huang et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)
B97-3c: A revised low-cost variant of the B97-D density functional method
Jan Gerit Brandenburg et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
Atom-Centered Potentials with Dispersion-Corrected Minimal-Basis-Set Hartree-Fock: An Efficient and Accurate Computational Approach for Large Molecular Systems
Viki Kumar Prasad et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Toward Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set
Jan Rezac et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Jing Huang et al.
NATURE METHODS (2017)
Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C
Jonathon Witte et al.
JOURNAL OF CHEMICAL PHYSICS (2017)
The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions
Lori A. Burns et al.
JOURNAL OF CHEMICAL PHYSICS (2017)
Transferable Atom-Centered Potentials for the Correction of Basis Set Incompleteness Errors in Density-Functional Theory
A. Otero-de-la-Roza et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen
A. Krishnapriyan et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z=1-86)
Stefan Grimme et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15
Lee-Ping Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions
Lars Goerigk et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)
ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules
Justin S. Smith et al.
SCIENTIFIC DATA (2017)
Small Bioactive Peptides for Biomaterials Design and Therapeutics
I. W. Hamley
CHEMICAL REVIEWS (2017)
Benchmark ab Initio Conformational Energies for the Proteinogenic Amino Acids through Explicitly Correlated Methods. Assessment of Density Functional Methods
Manoj K. Kesharwani et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources
Rebecca Sure et al.
CHEMISTRYOPEN (2016)
Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications
Anders S. Christensen et al.
CHEMICAL REVIEWS (2016)
Assessing the Accuracy of Across-the-Scale Methods for Predicting Carbohydrate Conformational Energies for the Examples of Glucose and α-Maltose
Mateusz Marianski et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters
Pavlo O. Dral et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Peptide Bond Isomerization in High-Temperature Simulations
Chris Neale et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Revised Damping Parameters for the D3 Dispersion Correction to Density Functional Theory
Daniel G. A. Smith et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2016)
Screened exchange hybrid density functional for accurate and efficient structures and interaction energies
Jan Gerit Brandenburg et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2016)
The S66x8 benchmark for noncovalent interactions revisited: explicitly correlated ab initio methods and density functional theory
Brina Brauer et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2016)
The Cambridge Structural Database
Colin R. Groom et al.
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS (2016)
First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids
Matti Ropo et al.
SCIENTIFIC DATA (2016)
Consistent structures and interactions by density functional theory with small atomic orbital basis sets
Stefan Grimme et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins
Katarzyna Walczewska-Szewc et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
Michael J. Robertson et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit
Holger Kruse et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Halogen Bonding from Dispersion-Corrected Density-Functional Theory: The Role of De localization Error
A. Otero-de-la-Roza et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Conformational Equilibria in Butane-1,4-diol: A Benchmark of a Prototypical System with Strong Intramolecular H-bonds
Sebastian Kozuch et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2014)
Comprehensive Analysis of Energy Minima of the 20 Natural Amino Acids
Yongna Yuan et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2014)
Recommending Hartree-Fock Theory with London-Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures
Lars Goerigk et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
Low-Cost Quantum Chemical Methods for Noncovalent Interactions
Jan Gerit Brandenburg et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)
Semiempirical quantum-chemical methods
Walter Thiel
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2014)
Non-covalent interactions and thermochemistry using XDM-corrected hybrid and range-separated hybrid density functionals
A. Otero-de-la-Roza et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Natural triple excitations in local coupled cluster calculations with pair natural orbitals
Christoph Riplinger et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
An efficient and near linear scaling pair natural orbital based local coupled cluster method
Christoph Riplinger et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the Gold Standard, CCSD(T) at the Complete Basis Set Limit?
Jan Rezac et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Efficient Methods for the Quantum Chemical Treatment of Protein Structures: The Effects of London-Dispersion and Basis-Set Incompleteness on Peptide and Water-Cluster Geometries
Lars Goerigk et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins
Yue Shi et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Corrected small basis set Hartree-Fock method for large systems
Rebecca Sure et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters
James J. P. Stewart
JOURNAL OF MOLECULAR MODELING (2013)
The Melatonin Conformer Space: Benchmark and Assessment of Wave Function and DFT Methods for a Paradigmatic Biological and Pharmacological Molecule
Uma R. Fogueri et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2013)
Accurate quantum chemical energies for tetrapeptide conformations: why MP2 data with an insufficient basis set should be handled with caution
Lars Goerigk et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2013)
An overview of the Amber biomolecular simulation package
Romelia Salomon-Ferrer et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2013)
Freely Available Conformer Generation Methods: How Good Are They?
Jean-Paul Ebejer et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems
Holger Kruse et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods
Jan Rezac et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
Robert B. Best et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
Marcus D. Hanwell et al.
JOURNAL OF CHEMINFORMATICS (2012)
Wavefunction methods for noncovalent interactions
Edward G. Hohenstein et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2012)
Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries
Jan Rezac et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures
Jan Rezac et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals-Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions
Lars Goerigk et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Effect of the Damping Function in Dispersion Corrected Density Functional Theory
Stefan Grimme et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Open Babel: An open chemical toolbox
Noel M. O'Boyle et al.
JOURNAL OF CHEMINFORMATICS (2011)
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
Stefan Grimme et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set
Lucie Grafova et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
A General Database for Main Group Thermochemistry, Kinetics, and Noncovalent Interactions - Assessment of Common and Reparameterized (meta-)GGA Density Functionals
Lars Goerigk et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Density-functional tight-binding for beginners
Pekka Koskinen et al.
COMPUTATIONAL MATERIALS SCIENCE (2009)
Evaluation of Density Functionals and Basis Sets for Carbohydrates
Gabor I. Csonka et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes
Jan Rezac et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Conformers of Gaseous Cysteine
Jeremiah J. Wilke et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Performance of Ab Initio and Density Functional Methods for Conformational Equilibria of CnH2n+2 Alkane Isomers (n=4-8)
David Gruzman et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2009)
High temperature unfolding simulations of the TRPZ1 peptide
Giovanni Settanni et al.
BIOPHYSICAL JOURNAL (2008)
OMx-D: Semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application
Tell Tuttle et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field
Haydee Valdes et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
James J. P. Stewart
JOURNAL OF MOLECULAR MODELING (2007)
Exchange-hole dipole moment and the dispersion interaction revisited
Axel D. Becke et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
A unified density-functional treatment of dynamical, nondynamical, and dispersion correlations
Axel D. Becke et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Assessment of a long-range corrected hybrid functional
Oleg A. Vydrov et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Importance of short-range versus long-range Hartree-Fock exchange for the performance of hybrid density functionals
Oleg A. Vydrov et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
A post-Hartree-Fock model of intermolecular interactions: Inclusion of higher-order corrections
ER Johnson et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Exchange-hole dipole moment and the dispersion interaction: High-order dispersion coefficients
AD Becke et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
P Jurecka et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2006)
The Amber biomolecular simulation programs
DA Case et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
A density-functional model of the dispersion interaction
AD Becke et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
A post-Hartree-Fock model of intermolecular interactions
ER Johnson et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Exchange-hole dipole moment and the ospersion interaction
AD Becke et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
The Protein Data Bank
HM Berman et al.
NUCLEIC ACIDS RESEARCH (2000)