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。Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
James C. Gumbart et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations
Anita de Ruiter et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics
Michel Masella et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies
Anita de Ruiter et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Charging Free Energy Calculations Using the Generalized Solvent Boundary Potential (GSBP) and Periodic Boundary Condition: A Comparative Analysis Using Ion Solvation and Oxidation Free Energy in Proteins
Xiya Lu et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Exploring a charge-central strategy in the solution of Poisson's equation for biomolecular applications
Xingping Liu et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2013)
Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation
Nathan Schmid et al.
COMPUTER PHYSICS COMMUNICATIONS (2012)
Molecular Dynamics Investigation on a Series of HIV Protease Inhibitors: Assessing the Performance of MM-PBSA and MM-GBSA Approaches
Hemant Kumar Srivastava et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
Perspective: Alchemical free energy calculations for drug discovery
David L. Mobley et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors
Anita de Ruiter et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field
Maria M. Reif et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Assessment of the Intrinsic Conformational Preferences of Dipeptide Amino Acids in Aqueous Solution by Combined Umbrella Sampling/MBAR Statistics. A Comparison with Experimental Results
Victor L. Cruz et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies
Samuel Genheden et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2012)
Polarization effects in protein-ligand calculations extend farther than the actual induction energy
Paer Soederhjelm
THEORETICAL CHEMISTRY ACCOUNTS (2012)
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUS and a billion unknowns
Rio Yokota et al.
COMPUTER PHYSICS COMMUNICATIONS (2011)
Free energy calculations of protein-ligand interactions
Anita de Ruiter et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2011)
Alchemical free energy methods for drug discovery: progress and challenges
John D. Chodera et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)
Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies
Samuel Genheden et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Optimized Potential of Mean Force Calculations for Standard Binding Free Energies
Ignasi Buch et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0
Alpeshkumar K. Malde et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Charge Asymmetries in Hydration of Polar Solutes (vol 112, pg 2405, 2008)
David L. Mobley et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2011)
Thermodynamic, Diffusional, and Structural Anomalies in Rigid-Body Water Models
Manish Agarwal et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2011)
Towards Accurate Free Energy Calculations in Ligand Protein-Binding Studies
Thomas Steinbrecher et al.
CURRENT MEDICINAL CHEMISTRY (2010)
Accurate Estimates of Free Energy Changes in Charge Mutations
Brittany R. Morgan et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Effect of the Integration Method on the Accuracy and Computational Efficiency of Free Energy Calculations Using Thermodynamic Integration
Miguel Jorge et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
Julien Michel et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2010)
Hydration entropy of polar, nonpolar and charged species
Giuseppe Graziano
CHEMICAL PHYSICS LETTERS (2009)
An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
M. J. Harvey et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Efficient Free Energy Calculations on Small Molecule Host-Guest Systems-A Combined Linear Interaction Energy/One-Step Perturbation Approach
Chris Oostenbrink
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions
Maria M. Reif et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
Yuqing Deng et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Multilevel summation of electrostatic potentials using graphics processing units
David J. Hardy et al.
PARALLEL COMPUTING (2009)
Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions
Clara D. Christ et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Biased molecular simulations for free-energy mapping: A comparison on the KcsA channel as a test case
Enrico Piccinini et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins
Michele Cascella et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Binless estimation of the potential of mean force
Jodi E. Basner et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Charge asymmetries in hydration of polar solutes
David L. Mobley et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Anisotropic, polarizable molecular mechanics studies of inter- and intramoecular interactions and ligand-macromolecule complexes. A bottom-up strategy
Nohad Gresh et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Halide, ammonium, and alkali metal ion parameters for modeling aqueous solutions
Kasper P. Jensen et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Electrostatics calculations: latest methodological advances
P Koehl
CURRENT OPINION IN STRUCTURAL BIOLOGY (2006)
The GROMOS software for biomolecular simulation:: GROMOS05
M Christen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations -: art. no. 034107
TN Heinz et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Calculation of the redox potential of the protein azurin and some mutants
M van den Bosch et al.
CHEMBIOCHEM (2005)
Dependence of ion hydration on the sign of the ion's charge
A Grossfield
JOURNAL OF CHEMICAL PHYSICS (2005)
Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site
J Dolenc et al.
NUCLEIC ACIDS RESEARCH (2005)
Size dependent ion hydration, its asymmetry, and convergence to macroscopic behavior
S Rajamani et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods
MA Kastenholz et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
C Oostenbrink et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
A fast-Fourier transform method to solve continuum-electrostatics problems with truncated electrostatic interactions:: Algorithm and application to ionic solvation and ion-ion interaction
C Peter et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions:: A continuum electrostatics study
M Bergdorf et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Derivation of an improved simple point charge model for liquid water:: SPC/A and SPC/L
A Glättli et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
Free energy simulations come of age: Protein-ligand recognition
T Simonson et al.
ACCOUNTS OF CHEMICAL RESEARCH (2002)
Molecular dynamics applied to nucleic acids
J Norberg et al.
ACCOUNTS OF CHEMICAL RESEARCH (2002)
Solving the Poisson equation for solute-solvent systems using fast Fourier transforms
C Peter et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
On the charge and molecule based summations of solvent electrostatic potentials and the validity of electrostatic linear response in water
CS Babu et al.
JOURNAL OF BIOLOGICAL PHYSICS (2002)
Folding simulations of a three-stranded antiparallel β-sheet peptide
P Ferrara et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)
分享论文
