All-atom empirical potential for molecular modeling and dynamics studies of proteins (Q27860468)

scientific article (publication date: 30 April 1998)

Language	Label	Description	Also known as
English	All-atom empirical potential for molecular modeling and dynamics studies of proteins	scientific article (publication date: 30 April 1998)

Statements

instance of

scholarly article

0 references

title

All-atom empirical potential for molecular modeling and dynamics studies of proteins (English)

0 references

author

Martin Karplus

series ordinal

29

0 references

author name string

A D MacKerell

series ordinal

1

0 references

D Bashford

series ordinal

2

0 references

M Bellott

series ordinal

3

0 references

R L Dunbrack

series ordinal

4

0 references

J D Evanseck

series ordinal

5

0 references

M J Field

series ordinal

6

0 references

S Fischer

series ordinal

7

0 references

J Gao

series ordinal

8

0 references

H Guo

series ordinal

9

0 references

S Ha

series ordinal

10

0 references

D Joseph-McCarthy

series ordinal

11

0 references

L Kuchnir

series ordinal

12

0 references

K Kuczera

series ordinal

13

0 references

F T Lau

series ordinal

14

0 references

C Mattos

series ordinal

15

0 references

S Michnick

series ordinal

16

0 references

T Ngo

series ordinal

17

0 references

D T Nguyen

series ordinal

18

0 references

B Prodhom

series ordinal

19

0 references

W E Reiher

series ordinal

20

0 references

B Roux

series ordinal

21

0 references

M Schlenkrich

series ordinal

22

0 references

J C Smith

series ordinal

23

0 references

R Stote

series ordinal

24

0 references

J Straub

series ordinal

25

0 references

M Watanabe

series ordinal

26

0 references

J Wiórkiewicz-Kuczera

series ordinal

27

0 references

D Yin

series ordinal

28

0 references

language of work or name

English

0 references

publication date

30 April 1998

0 references

published in

Journal of Physical Chemistry B

0 references

volume

102

0 references

issue

18

0 references

page(s)

3586-616

0 references

cites work

Molecular dynamics simulations in biology

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Ab initio self-consistent field and potential-dependent partial equalization of orbital electronegativity calculations of hydration properties of N-acetyl-N'-methyl-alanineamide

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Crystal structure of myoglobin from a synthetic gene.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Accurate modeling of the intramolecular electrostatic energy of proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Rigid protein motion as a model for crystallographic temperature factors

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Role of structural flexibility in conformational calculations. Application to acetylcholine and .beta.-methylacetylcholine

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

A new force field for molecular mechanical simulation of nucleic acids and proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Conformation and crystal structure of the cyclic polypeptide [Gly-Gly-D-Ala-D-Ala-Gly-Gly] .3H2O

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

"New view" of protein folding reconciled with the old through multiple unfolding simulations.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Far-infrared spectra ofN-methylacetamide and related compounds and hydrogen-bond force constants

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Simulation of activation free energies in molecular systems

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Atomic resolution (0.83 A) crystal structure of the hydrophobic protein crambin at 130 K

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Comparison of simple potential functions for simulating liquid water

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Dynamics of folded proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Gas-phase IR spectra of substituted alkylamides

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

The missing term in effective pair potentials

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Molecular dynamics with coupling to an external bath

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Decisions in force field development: an alternative to those described by Roterman et al. (J. Biomol. Struct. Dyn. 7, 421 (1989)).

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

DREIDING: a generic force field for molecular simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

First-principles calculation of the folding free energy of a three-helix bundle protein

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

An all atom force field for simulations of proteins and nucleic acids

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Deviations from planarity of the peptide bond in peptides and proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Protein dynamics in solution and in a crystalline environment: a molecular dynamics study

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

L-alanyl-L-alanyl-L-alanine: parallel pleated sheet arrangement in unhydrated crystal structure, and comparisons with the antiparallel sheet structure

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

A sequence preference for nucleation of alpha-helix--crystal structure of Gly-L-Ala-L-Val and Gly-L-Ala-L-Leu: some comments on the geometry of leucine zippers

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Comparison of the dynamics of myoglobin in different crystal forms

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Molecular force field and structure of water: Recent microwave results

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Temperature dependence of dynamics of hydrated myoglobin. Comparison of force field calculations with neutron scattering data

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Direct observation of protein solvation and discrete disorder with experimental crystallographic phases

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

Hydrogen bonding in globular proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP973084F

All-atom empirical potential for molecular modeling and dynamics studies of proteins (Q27860468)

Statements

Identifiers

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Navigation menu

All-atom empirical potential for molecular modeling and dynamics studies of proteins (Q27860468)

Statements

Identifiers

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Navigation menu

Search