Two-dimensional replica-exchange method for predicting protein-ligand binding structures (Q57905834)

Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes

21 January 2018

1 reference

Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking

21 January 2018

1 reference

Computer-aided drug-discovery techniques that account for receptor flexibility

21 January 2018

1 reference

Large conformational changes in proteins: signaling and other functions

21 January 2018

1 reference

Principles that govern the folding of protein chains

21 January 2018

1 reference

The protein folding problem

21 January 2018

1 reference

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

21 January 2018

1 reference

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

21 January 2018

1 reference

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

21 January 2018

1 reference

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation

21 January 2018

1 reference

Prediction of membrane protein structures by replica-exchange Monte Carlo simulations: case of two helices.

21 January 2018

1 reference

Prediction of transmembrane helix configurations by replica-exchange simulations

21 January 2018

1 reference

Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange Monte Carlo simulation

21 January 2018

1 reference

Analysis of helix-helix interactions of bacteriorhodopsin by replica-exchange simulations

21 January 2018

1 reference

Hydrophobic Core Formation and Dehydration in Protein Folding Studied by Generalized-Ensemble Simulations

21 January 2018

1 reference

Atomic-Level Characterization of the Structural Dynamics of Proteins

21 January 2018

1 reference

Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations

21 January 2018

1 reference

Multidimensional replica-exchange method for free-energy calculations

21 January 2018

1 reference

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

21 January 2018

1 reference

Coulomb replica-exchange method: handling electrostatic attractive and repulsive forces for biomolecules

21 January 2018

1 reference

Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation.

21 January 2018

1 reference

Replica exchange with solute tempering: a method for sampling biological systems in explicit water

21 January 2018

1 reference

Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).

21 January 2018

1 reference

On easy implementation of a variant of the replica exchange with solute tempering in GROMACS.

21 January 2018

1 reference

Replica-Permutation Method with the Suwa-Todo Algorithm beyond the Replica-Exchange Method

21 January 2018

1 reference

Markov chain Monte Carlo method without detailed balance.

21 January 2018

1 reference

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

Statistically optimal analysis of samples from multiple equilibrium states

21 January 2018

1 reference

Optimal protocol and trajectory visualization for conformational searches of peptides and proteins

21 January 2018

1 reference

Essential dynamics of proteins

21 January 2018

1 reference

Investigating protein dynamics in collective coordinate space

21 January 2018

1 reference

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

21 January 2018

1 reference

Dependency of ligand free energy landscapes on charge parameters and solvent models

21 January 2018

1 reference

21 January 2018

The Protein Data Bank

1 reference

Automatic atom type and bond type perception in molecular mechanical calculations

21 January 2018

1 reference

Development and testing of a general amber force field

21 January 2018

1 reference

The Amber biomolecular simulation programs

21 January 2018

1 reference

Comparison of multiple Amber force fields and development of improved protein backbone parameters

21 January 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

The statistical-thermodynamic basis for computation of binding affinities: a critical review

21 January 2018

1 reference

Calculation of protein-ligand binding affinities.

21 January 2018

1 reference

Preferential solvation in urea solutions at different concentrations: properties from simulation studies

21 January 2018

1 reference

Molecular basis of the apparent near ideality of urea solutions

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/JCC.23427

0 references

DBLP publication ID

journals/jcc/KokuboTO13

1 reference

DBLP Dataset 2021-01-02