(Q35878947)

10 August 2017

Automation of AMOEBA polarizable force field parameterization for small molecules (English)

1 reference

10 August 2017

0 references

1 reference

Johnny C Wu

1

1 reference

10 August 2017

Gaurav Chattree

series ordinal

2

1 reference

10 August 2017

Pengyu Ren

series ordinal

3

1 reference

10 August 2017

1 February 2012

1 reference

Theoretical Chemistry Accounts

10 August 2017

1 reference

10 August 2017

131

1 reference

10 August 2017

3

1 reference

10 August 2017

1138

1 reference

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Incorporating Phase-Dependent Polarizability in Non-Additive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid-Vapor Interface

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Polarization effects in molecular mechanical force fields

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Multipole electrostatics in hydration free energy calculations

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Current status of the AMOEBA polarizable force field

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Trypsin-ligand binding free energy calculation with AMOEBA.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

QM/MM methods for biomolecular systems

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Calculation of protein-ligand binding free energy by using a polarizable potential

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

The determination of protonation states in proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Automatic atom type and bond type perception in molecular mechanical calculations

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Development and testing of a general amber force field

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Ab initio calculations of structures and interaction energies of toluene dimers including CCSD(T) level electron correlation correction

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Ion solvation thermodynamics from simulation with a polarizable force field

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322661

SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

24 September 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00214-012-1138-6

The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00214-012-1138-6

Distributed multipole analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00214-012-1138-6

Model for Aqueous Solvation Based on Class IV Atomic Charges and First Solvation Shell Effects

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00214-012-1138-6

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00214-012-1138-6

Aqueous Solvation Free Energies of Ions and Ion−Water Clusters Based on an Accurate Value for the Absolute Aqueous Solvation Free Energy of the Proton

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00214-012-1138-6

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00214-012-1138-6

Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: NonempiricalAb InitioCalculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00214-012-1138-6

Distributed Multipole Analysis: Stability for Large Basis Sets

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22505837

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22505837

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Fluctuation attraction in condensed matter: A nonlocal functional approach

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22505837

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S00214-012-1138-6

1 reference

10 August 2017

1 reference

10 August 2017

PubMed publication ID

22505837

1 reference