Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition (Q35794917)

10 August 2017

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition (English)

1 reference

10 August 2017

0 references

2

J Andrew McCammon

1 reference

10 August 2017

Jeff Wereszczynski

1

1 reference

PubMed ID

22082669

10 August 2017

language of work or name

1 reference

15 November 2011

1 reference

Quarterly Reviews of Biophysics

10 August 2017

1 reference

10 August 2017

45

1 reference

10 August 2017

1

1 reference

10 August 2017

1-25

1 reference

Modeling Protein-Ligand Binding by Mining Minima

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

A displaced-solvent functional analysis of model hydrophobic enclosures

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Molecular binding: Under water's influence

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

How Can Hydrophobic Association Be Enthalpy Driven?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Water in cavity-ligand recognition

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Long-timescale molecular-dynamics simulations of the major urinary protein provide atomistic interpretations of the unusual thermodynamics of ligand binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: analysis of the epidermal growth factor-like repeat A docking site using WaterMap

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Prediction of the water content in protein binding sites

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Theory of free energy and entropy in noncovalent binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

High-energy water sites determine peptide binding affinity and specificity of PDZ domains

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

λ-Dynamics free energy simulation methods

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Computational evaluation of protein-small molecule binding.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Statistically optimal analysis of samples from multiple equilibrium states

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Are current molecular dynamics force fields too helical?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

MM-GB/SA rescoring of docking poses in structure-based lead optimization.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Accelerating molecular modeling applications with graphics processors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Predicting absolute ligand binding free energies to a simple model site

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Calculation of protein-ligand binding affinities.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Virtual ligand screening: strategies, perspectives and limitations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Free energies of ligand binding for structurally diverse compounds

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Docking and scoring in virtual screening for drug discovery: methods and applications

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Empirical force fields for biological macromolecules: overview and issues.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Molecular recognition and docking algorithms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Escaping free-energy minima

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

A model binding site for testing scoring functions in molecular docking

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Introduction: Molecular Recognition

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Cooperativity in drug-DNA recognition: a molecular dynamics study

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

AKAPs: from structure to function

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

A new class of models for computing receptor-ligand binding affinities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Sensing the heat: the application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Fluctuations in Protein Structure from X-Ray Diffraction

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: A ubiquitous properly of water

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Evaluating the Accuracy of the Quasiharmonic Approximation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Multiple free energies from a single simulation: extending enveloping distribution sampling to nonoverlapping phase-space distributions.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

A molecular dynamics approach to study the importance of solvent in protein interactions

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Adaptive biasing force method for scalar and vector free energy calculations

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Induction of flexibility through protein-protein interactions

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Theory of biomolecular recognition

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3291752

Anton, a special-purpose machine for molecular dynamics simulation

25 September 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583511000096

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583511000096

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583511000096

Effect of the Integration Method on the Accuracy and Computational Efficiency of Free Energy Calculations Using Thermodynamic Integration

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583511000096

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583511000096

The Development of Replica-Exchange-Based Free-Energy Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583511000096

Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme

21 January 2018

1 reference

12 December 2020

Calculations of solute and solvent entropies from molecular dynamics simulations

1 reference

12 December 2020

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

1 reference

12 December 2020

Direct observation of salt effects on molecular interactions through explicit-solvent molecular dynamics simulations: differential effects on electrostatic and hydrophobic interactions and comparisons to Poisson-Boltzmann theory

1 reference

12 December 2020

Improving Docking Accuracy through Molecular Mechanics Generalized Born Optimization and Scoring

1 reference

12 December 2020

Absolute free energy calculations by thermodynamic integration in four spatial dimensions

1 reference

12 December 2020

Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring

1 reference

12 December 2020

NMR relaxation studies of the role of conformational entropy in protein stability and ligand binding

1 reference

12 December 2020

Absolute and relative entropies from computer simulation with applications to ligand binding

1 reference

12 December 2020

Increased protein backbone conformational entropy upon hydrophobic ligand binding

1 reference

12 December 2020

Enveloping distribution sampling: a method to calculate free energy differences from a single simulation

1 reference

12 December 2020

Absolute Binding Free Energies: A Quantitative Approach for Their Calculation

1 reference

https://api.crossref.org/works/10.1017%2FS0033583511000096

7 January 2021

inferred from DOI database lookup

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

1 reference

https://api.crossref.org/works/10.1017%2FS0033583511000096

7 January 2021

inferred from DOI database lookup

How accurate can molecular dynamics/linear response and Poisson-Boltzmann/solvent accessible surface calculations be for predicting relative binding affinities? Acetylcholinesterase huprine inhibitors as a test case

1 reference

https://api.crossref.org/works/10.1017%2FS0033583511000096

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1017/S0033583511000096

1 reference

10 August 2017

1 reference

10 August 2017

1 reference

PubMed ID

22082669