(Q38770768)

6 September 2017

Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package (English)

1 reference

6 September 2017

4

David A Case

0 references

Marcus Elstner

series ordinal

3

object named as

Marcus Elstner

1 reference

6 September 2017

5

Adrian E Roitberg

1 reference

6 September 2017

Gustavo de M Seabra

1

1 reference

6 September 2017

Ross C Walker

series ordinal

2

1 reference

6 September 2017

David A Case

series ordinal

4

1 reference

6 September 2017

language of work or name

English

0 references

publication date

24 May 2007

1 reference

Journal of Physical Chemistry A

6 September 2017

1 reference

6 September 2017

111

1 reference

6 September 2017

26

1 reference

6 September 2017

5655-5664

1 reference

Conformational preferences of non-prolyl and prolyl residues.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Comparison of multiple Amber force fields and development of improved protein backbone parameters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Intrinsic backbone preferences are fully present in blocked amino acids

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Catalytic reaction mechanism of homogentisate dioxygenase: a hybrid DFT study

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Polyproline II propensities from GGXGG peptides reveal an anticorrelation with beta-sheet scales

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

The Amber biomolecular simulation programs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Generalized-ensemble algorithms for molecular simulations of biopolymers

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

How enzyme dynamics helps catalyze a reaction in atomic detail: a transition path sampling study

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

A molecular dynamics study of the dielectric properties of aqueous solutions of alanine and alanine dipeptide

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Assessing the reliability of density functional methods in the conformational study of polypeptides: the treatment of intraresidue nonbonding interactions

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

PDDG/PM3 and PDDG/MNDO: improved semiempirical methods.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

Conformational dynamics of an alanine dipeptide analog: an ab initio molecular dynamics study

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

An Efficienta PosterioriTreatment for Dispersion Interaction in Density-Functional-Based Tight Binding

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3197852

A Critical Evaluation of Different QM/MM Frontier Treatments with SCC-DFTB as the QM Method

3 December 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Importance of van der Waals Interactions in QM/MM Simulations

1 reference

12 December 2020

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

1 reference

12 December 2020

Elucidating the mechanism for the reduction of nitrite by copper nitrite reductase--a contribution from quantum chemical studies

1 reference

12 December 2020

Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?

1 reference

12 December 2020

Two-dimensional infrared spectroscopy of the alanine dipeptide in aqueous solution

1 reference

12 December 2020

The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding method

1 reference

12 December 2020

Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP070071L

1 reference

6 September 2017

1 reference

6 September 2017

PubMed publication ID

17521173

1 reference