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Molecular dynamics: survey of methods for simulating the activity of proteins

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Europe PubMed Central

PMC publication ID

14 August 2017

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Europe PubMed Central

Molecular dynamics: survey of methods for simulating the activity of proteins (English)

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Europe PubMed Central

PMC publication ID

14 August 2017

J. Andrew McCammon

2

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J Andrew McCammon

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

author name string

Stewart A Adcock

1

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

publication date

1 May 2006

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Europe PubMed Central

PMC publication ID

14 August 2017

Chemical Reviews

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Europe PubMed Central

PMC publication ID

14 August 2017

106

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

5

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

1589-1615

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

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Optimization by Simulated Annealing

1 reference

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Theoretical and computational models of biological ion channels

1 reference

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30 September 2017

Implicit solvent models

1 reference

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Protein folding-simulation

1 reference

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Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis

1 reference

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The Amber biomolecular simulation programs

1 reference

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Molecular dynamics simulations of proteins in lipid bilayers

1 reference

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Enhancing the accuracy, the efficiency and the scope of free energy simulations

1 reference

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Biomolecular simulations at constant pH.

1 reference

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Long-timescale simulation methods

1 reference

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Coarse-grained models for proteins

1 reference

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Improving implicit solvent simulations: a Poisson-centric view

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A naphthyridine carboxamide provides evidence for discordant resistance between mechanistically identical inhibitors of HIV-1 integrase

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Empirical force fields for biological macromolecules: overview and issues.

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CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

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A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions

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The simulation approach to bacterial outer membrane proteins.

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Simulation and modeling of nucleic acid structure, dynamics and interactions

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Binding affinity prediction with different force fields: examination of the linear interaction energy method

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Development and testing of a general amber force field

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Recent advances in the development and application of implicit solvent models in biomolecule simulations

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Discovery of a novel binding trench in HIV integrase.

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Structural interpretation of pH and salt-dependent processes in proteins with computational methods

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Conformational sampling for the impatient

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Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

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Refinement of homology-based protein structures by molecular dynamics simulation techniques

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The role of dynamics in allosteric regulation

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30 September 2017

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

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All-atom simulations of protein folding and unfolding

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Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress

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Protein simulation and drug design

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Force fields for protein simulations

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Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics

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Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.

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Molecular dynamics simulations of peptides and proteins with amplified collective motions

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Thermodynamics of protein folding: a microscopic view

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Molecular dynamics studies of the wild-type and double mutant HIV-1 integrase complexed with the 5CITEP inhibitor: mechanism for inhibition and drug resistance

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Molecular recognition and docking algorithms

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Refinement of protein structures in explicit solvent

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Absolute comparison of simulated and experimental protein-folding dynamics

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On the calculation of absolute macromolecular binding free energies

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Protein flexibility and computer-aided drug design

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30 September 2017

Molecular dynamics applied to nucleic acids

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Protein flexibility is an important component of structure-based drug discovery.

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ATP-bound states of GroEL captured by cryo-electron microscopy

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Steered molecular dynamics investigations of protein function.

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Polarizable force fields

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Molecular dynamics simulation of nucleic acids

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Site-directed ligand discovery

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Developing a dynamic pharmacophore model for HIV-1 integrase.

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Collective protein dynamics in relation to function

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Accommodating protein flexibility in computational drug design

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Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design

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De novo protein design. I. In search of stability and specificity.

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Molecular dynamics simulations of biomolecules: long-range electrostatic effects

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Molecular dynamics studies on the HIV-1 integrase catalytic domain

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30 September 2017

Atomic force microscope

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Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

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The M2 channel of influenza A virus: a molecular dynamics study

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The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Reconstructing potential energy functions from simulated force-induced unbinding processes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Dynamic strength of molecular adhesion bonds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Discovering high-affinity ligands for proteins: SAR by NMR

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Molecular dynamics: deciphering the data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

VMD: visual molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Automated docking of flexible ligands: applications of AutoDock

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Computational methods to predict binding free energy in ligand-receptor complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Protein hydration elucidated by molecular dynamics simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Prediction of pH-dependent properties of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Restoring allosterism with compensatory mutations in hemoglobin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Classical electrostatics in biology and chemistry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Local elevation: a method for improving the searching properties of molecular dynamics simulation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Theory of electrostatic interactions in macromolecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Simulation methods for protein structure fluctuations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Minimization of polypeptide energy. 8. Application of the deflation technique to a dipeptide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Optical trapping and manipulation of viruses and bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Theoretical calculation of relative binding affinity in host-guest systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Filtering molecular dynamics trajectories to reveal low-frequency collective motions: phospholipase A2.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Molecular dynamics studies of a DNA‐binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Dynamics of folded proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Novel methods of sampling phase space in the simulation of biological systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

30 September 2017

Understanding the determinants of stability and folding of small globular proteins from their energetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

28 June 2018

Multiple grid methods for classical molecular dynamics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

28 June 2018

Flexible ligand docking: a multistep strategy approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

28 June 2018

Cooperative fluctuations and subunit communication in tryptophan synthase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

28 June 2018

Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

28 June 2018

The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

28 June 2018

Multiple time step diffusive Langevin dynamics for proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

28 June 2018

Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experimentation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

28 June 2018

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

28 June 2018

Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

28 June 2018

Interactive essential dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

BioSimGrid: towards a worldwide repository for biomolecular simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Constant pH molecular dynamics in generalized Born implicit solvent

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Automatic domain decomposition of proteins by a Gaussian Network Model.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Rate constants for diffusive processes by partial path sampling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Computing time scales from reaction coordinates by milestoning.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

An alternative multipolar expansion for intermolecular potential functions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Structural basis for cooperative DNA binding by CAP and lac repressor.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Ion solvation thermodynamics from simulation with a polarizable force field

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Automated generation of MCSS-derived pharmacophoric DOCK site points for searching multiconformation databases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Exploring the natural conformational changes of the C-terminal domain of calmodulin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Contributions to the binding free energy of ligands to avidin and streptavidin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Time-trimming tricks for dynamic simulations: splitting force updates to reduce computational work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

MCSS functionality maps for a flexible protein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Protein hydration density: theory, simulations and crystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

A structure refinement method based on molecular dynamics in four spatial dimensions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Protein electrostatics: rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Molecular dynamics simulation of the docking of substrates to proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Functionality maps of binding sites: a multiple copy simultaneous search method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 September 2018

Prediction of protein conformational freedom from distance constraints

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

21 October 2018

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2547409

4 December 2018

Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Conformational sampling using high-temperature molecular dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Computer simulations of protein folding by targeted molecular dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular simulations of diffusion and association in multimacromolecular systems

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Free energy grids: a practical qualitative application of free energy perturbation to ligand design using the OWFEG method

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Poisson–Boltzmann Methods for Biomolecular Electrostatics

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Computational studies of ligand diffusion in globins: I. Leghemoglobin

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Langevin dynamics of proteins at constant pH

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular modeling of interleukin-8 receptor beta and analysis of the receptor-ligand interaction

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mathematical analysis of coupled parallel simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Predicting slow structural transitions in macromolecular systems: Conformational flooding

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Large-amplitude nonlinear motions in proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Improved scoring of ligand-protein interactions using OWFEG free energy grids

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

https://pubmed.ncbi.nlm.nih.gov/16683746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Zur Quantentheorie der Molekeln

1 reference

https://opencitations.net/index/coci/api/v1/citations/10.1002/ANDP.19273892002

29 July 2023

Identifiers

10.1021/CR040426M

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

ResearchGate publication ID

0 references

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