(Q43063613)

13 November 2017

Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations (English)

1 reference

13 November 2017

1 reference

3

Charles L Brooks

1 reference

13 November 2017

Kira A Armacost

1

1 reference

PMC publication ID

4731093

13 November 2017

Garrett B Goh

series ordinal

2

1 reference

13 November 2017

1 March 2015

1 reference

Journal of Chemical Theory and Computation

13 November 2017

1 reference

13 November 2017

11

1 reference

13 November 2017

3

1 reference

13 November 2017

1267-1277

1 reference

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors

13 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Practical Aspects of Free-Energy Calculations: A Review

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Lead optimization mapper: automating free energy calculations for lead optimization

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Contributions of co-chaperones and post-translational modifications towards Hsp90 drug sensitivity

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Synthesis of 19-substituted geldanamycins with altered conformations and their binding to heat shock protein Hsp90

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Molecular recognition and ligand association

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

The therapeutic target Hsp90 and cancer hallmarks

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Multi-Site λ-dynamics for simulated Structure-Activity Relationship studies

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

MATCH: an atom-typing toolset for molecular mechanics force fields.

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Molecular dynamics simulations and drug discovery

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Open Babel: An open chemical toolbox

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Applying efficient implicit nongeometric constraints in alchemical free energy simulations

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD).

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Alchemical free energy methods for drug discovery: progress and challenges

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Targeting the dynamic HSP90 complex in cancer

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

CHARMM: the biomolecular simulation program

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

λ-Dynamics free energy simulation methods

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Potent cytotoxic C-11 modified geldanamycin analogues

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Calculation of protein-ligand binding affinities.

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Synthesis and biological activities of novel 17-aminogeldanamycin derivatives

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Synthesis and biological evaluation of a new class of geldanamycin derivatives as potent inhibitors of Hsp90.

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

The many roles of computation in drug discovery

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Crystal structure and molecular modeling of 17-DMAG in complex with human Hsp90

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Chemoinformatics - similarity and diversity in chemical libraries

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Crystal structure of an Hsp90-geldanamycin complex: targeting of a protein chaperone by an antitumor agent

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

An improved route to 19-substituted geldanamycins as novel Hsp90 inhibitors--potential therapeutics in cancer and neurodegeneration

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Temperature weighted histogram analysis method, replica exchange, and transition paths.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4731093

A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling

15 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26579773

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Free energy calculations by computer simulation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26579773

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26579773

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT500894K

1 reference

13 November 2017

1 reference

PMC publication ID

4731093

13 November 2017

PubMed publication ID

26579773

1 reference

PMC publication ID

4731093