(Q30417026)

17 October 2017

Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization (English)

1 reference

17 October 2017

Junmei Wang

1

0 references

Ray Luo

object named as

Ray Luo

6

0 references

author name string

Piotr Cieplak

2

1 reference

17 October 2017

Jie Li

3

1 reference

17 October 2017

Qin Cai

4

1 reference

17 October 2017

Meng-Juei Hsieh

5

1 reference

17 October 2017

Yong Duan

7

1 reference

17 October 2017

language of work or name

English

0 references

publication date

6 June 2012

1 reference

Journal of Physical Chemistry B

17 October 2017

14

1 reference

based on heuristic

inferred from page(s)

published in

1 reference

17 October 2017

116

1 reference

17 October 2017

24

1 reference

17 October 2017

7088-7101

1 reference

Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

17 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Polarization effects in molecular mechanical force fields

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Automatic atom type and bond type perception in molecular mechanical calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Validation of the 53A6 GROMOS force field

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Development and testing of a general amber force field

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Force fields for protein simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Langevin stabilization of molecular-dynamics simulations of polymers by means of quasisymplectic algorithms.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Genetic algorithm-optimized QSPR models for bioavailability, protein binding, and urinary excretion.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3391542

Synchronization of trajectories in canonical molecular-dynamics simulations: observation, explanation, and exploitation

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22612331

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22612331

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JP3019759

1 reference

17 October 2017

1 reference

17 October 2017

PubMed publication ID

22612331

1 reference