Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. (Q41339143)

29 September 2017

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. (English)

1 reference

29 September 2017

Steven Ramsey

1

1 reference

29 September 2017

Crystal Nguyen

2

1 reference

29 September 2017

Romelia Salomon-Ferrer

3

1 reference

29 September 2017

Ross C Walker

4

1 reference

29 September 2017

Michael K Gilson

5

1 reference

29 September 2017

Tom Kurtzman

6

1 reference

29 September 2017

18 June 2016

1 reference

Journal of Computational Chemistry

29 September 2017

1 reference

29 September 2017

37

1 reference

29 September 2017

21

1 reference

29 September 2017

2029-2037

1 reference

SPAM: A Simple Approach for Profiling Bound Water Molecules

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Interactions between Hofmeister anions and the binding pocket of a protein

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Water networks contribute to enthalpy/entropy compensation in protein-ligand binding

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

The binding of benzoarylsulfonamide ligands to human carbonic anhydrase is insensitive to formal fluorination of the ligand

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Accounting for water molecules in drug design

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Computer-aided drug design of falcipain inhibitors: virtual screening, structure-activity relationships, hydration site thermodynamics, and reactivity analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

A displaced-solvent functional analysis of model hydrophobic enclosures

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Molecular binding: Under water's influence

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Water in cavity-ligand recognition

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

A medicinal chemist's guide to molecular interactions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Prediction of the water content in protein binding sites

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Molecular modeling of hydration in drug design.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Complexation of ferrocene derivatives by the cucurbit[7]uril host: a comparative study of the cucurbituril and cyclodextrin host families

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Development and testing of a general amber force field

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Molecular structures of human factor Xa complexed with ketopiperazine inhibitors: preference for a neutral group in the S1 pocket

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

VMD: visual molecular dynamics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Accurate Estimation of the Entropy of Rotation-Translation Probability Distributions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

WATsite: hydration site prediction program with PyMOL interface

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Estimating Translational and Orientational Entropies Using the k-Nearest Neighbors Algorithm

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Contributions of water transfer energy to protein-ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): theory and application.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Thermodynamics of buried water clusters at a protein-ligand binding interface

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Including tightly-bound water molecules in de novo drug design. Exemplification through the in silico generation of poly(ADP-ribose)polymerase ligands.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Solvent size vs cohesive energy as the origin of hydrophobicity

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052087

Free enthalpies of replacing water molecules in protein binding pockets

19 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FJCC.24417

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FJCC.24417

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FJCC.24417

Computing the thermodynamic contributions of interfacial water

21 January 2018

1 reference

12 December 2020

Water molecules in a protein cavity detected by a statistical-mechanical theory

1 reference

12 December 2020

Thermodynamic contributions of the ordered water molecule in HIV-1 protease

1 reference

12 December 2020

WATCLUST: a tool for improving the design of drugs based on protein-water interactions

1 reference

12 December 2020

Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions

1 reference

12 December 2020

Identifiers

DOI

10.1002/JCC.24417

1 reference

journals/jcc/RamseyNSWGK16

29 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

29 September 2017

PubMed publication ID

27317094

1 reference