Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: Application to the DNA binding domain of lac repressor fromEscherichia coli

J. de Vlieg; R. M. Scheek; W. F. van Gunsteren; H. J. C. Berendsen; R. Kaptein; J. Thomason

doi:10.1002/prot.340030402

Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: Application to the DNA binding domain of lac repressor fromEscherichia coli

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.340030402 ◽

1988 ◽

Vol 3 (4) ◽

pp. 209-218 ◽

Cited By ~ 52

Author(s):

J. de Vlieg ◽

R. M. Scheek ◽

W. F. van Gunsteren ◽

H. J. C. Berendsen ◽

R. Kaptein ◽

...

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Distance Geometry ◽

Protein Structure Determination ◽

Lac Repressor ◽

Dna Binding Domain ◽

Combined Procedure ◽

Magnetic Resonance Data ◽

Data Application ◽

Resonance Data

Determination of protein structures from nuclear magnetic resonance data using a restrained molecular dynamics approach: The lac repressor DNA binding domain

Biochimie ◽

10.1016/s0300-9084(85)80158-9 ◽

1985 ◽

Vol 67 (7-8) ◽

pp. 707-715 ◽

Cited By ~ 43

Author(s):

E ZUIDERWEG ◽

R SCHEEK ◽

R BOELENS ◽

W VANGUNSTEREN ◽

R KAPTEIN

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Dna Binding ◽

Protein Structures ◽

Lac Repressor ◽

Dna Binding Domain ◽

Magnetic Resonance Data ◽

Resonance Data

[14] Combined procedures of distance geometry and molecular dynamics for determining protein structure from nuclear magnetic resonance data

Methods in Enzymology - Molecular Design and Modeling: Concepts and Applications Part A: Proteins, Peptides, and Enzymes ◽

10.1016/0076-6879(91)02016-3 ◽

1991 ◽

pp. 268-300 ◽

Cited By ~ 14

Author(s):

Jacob De Vlieg ◽

Wilfred F. Van Gunsteren

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Protein Structure ◽

Magnetic Resonance ◽

Distance Geometry ◽

Nuclear Magnetic Resonance Data ◽

Combined Procedures ◽

Magnetic Resonance Data ◽

Resonance Data ◽

Nuclear Magnetic

DISCO—a general computer program for the computation of acid dissociation constants of polyprotic molecules in water and biological fluids, from nuclear magnetic resonance data: application to polyamines

Analytical Biochemistry ◽

10.1016/s0003-2697(03)00300-2 ◽

2003 ◽

Vol 319 (2) ◽

pp. 179-194 ◽

Cited By ~ 5

Author(s):

Fabiano Reniero ◽

Claude Guillou ◽

Chiara Frassineti ◽

Stefano Ghelli

Keyword(s):

Nuclear Magnetic Resonance ◽

Dissociation Constants ◽

Biological Fluids ◽

Acid Dissociation ◽

Acid Dissociation Constants ◽

Magnetic Resonance Data ◽

Data Application ◽

Resonance Data ◽

General Computer Program ◽

General Computer

Protein Unfolding Transitions in an Intrinsically Unstable Annexin Domain: Molecular Dynamics Simulation and Comparison with Nuclear Magnetic Resonance Data

Biophysical Journal ◽

10.1016/s0006-3495(02)75200-4 ◽

2002 ◽

Vol 83 (2) ◽

pp. 681-698 ◽

Cited By ~ 6

Author(s):

Tru Huynh ◽

Jeremy C. Smith ◽

Alain Sanson

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Molecular Dynamics Simulation ◽

Magnetic Resonance ◽

Protein Unfolding ◽

Nuclear Magnetic Resonance Data ◽

Dynamics Simulation ◽

Magnetic Resonance Data ◽

Resonance Data ◽

Nuclear Magnetic

Molecular dynamics simulation of hen egg white lysozyme: A test of the GROMOS96 force field against nuclear magnetic resonance data

Proteins Structure Function and Bioinformatics ◽

10.1002/(sici)1097-0134(20000701)40:1<145::aid-prot160>3.0.co;2-y ◽

2000 ◽

Vol 40 (1) ◽

pp. 145-153 ◽

Cited By ~ 61

Author(s):

Urs Stocker ◽

Wilfred F. van Gunsteren

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Egg White ◽

Dynamics Simulation ◽

Hen Egg White Lysozyme ◽

Egg White Lysozyme ◽

Magnetic Resonance Data ◽

Resonance Data ◽

Hen Egg White ◽

Hen Egg

Raw nuclear magnetic resonance data of human linker histone H1x, lacking the C-terminal domain (NGH1x), and trajectory data of nanosecond molecular dynamics simulations of GH1x- and NGH1x-chromatosomes

Data in Brief ◽

10.1016/j.dib.2020.105865 ◽

2020 ◽

Vol 31 ◽

pp. 105865

Author(s):

Herna de Wit ◽

Alicia Vallet ◽

Bernhard Brutscher ◽

Leon du Preez ◽

Gerrit Koorsen

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Molecular Dynamics Simulations ◽

Linker Histone ◽

Nuclear Magnetic Resonance Data ◽

Trajectory Data ◽

Magnetic Resonance Data ◽

Resonance Data ◽

Dynamics Simulations

[10] Molecular dynamics simulation techniques for determination of molecular structures from nuclear magnetic resonance data

Methods in Enzymology - Nuclear Magnetic Resonance Part B Structure and Mechanism ◽

10.1016/0076-6879(89)77012-9 ◽

1989 ◽

pp. 204-218 ◽

Cited By ~ 75

Author(s):

R.M. Scheek ◽

W.F. van Gunsteren ◽

R. Kaptein

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Molecular Dynamics Simulation ◽

Magnetic Resonance ◽

Molecular Structures ◽

Dynamics Simulation ◽

Magnetic Resonance Data ◽

Simulation Techniques ◽

Resonance Data

Scaled Alternating Steepest Descent Algorithm Applied for Protein Structure Determination from Nuclear Magnetic Resonance Data

Journal of Computational Biology ◽

10.1089/cmb.2019.0013 ◽

2019 ◽

Vol 26 (9) ◽

pp. 1020-1029 ◽

Cited By ~ 1

Author(s):

Zhicheng Li ◽

Shijian Li ◽

Xian Wei ◽

Qing Zhao

Keyword(s):

Nuclear Magnetic Resonance ◽

Protein Structure ◽

Magnetic Resonance ◽

Structure Determination ◽

Protein Structure Determination ◽

Steepest Descent ◽

Descent Algorithm ◽

Magnetic Resonance Data ◽

Resonance Data ◽

Steepest Descent Algorithm

Determination of the stereochemistry of natural products from nuclear magnetic resonance data by constrained molecular dynamics

Journal of Computational Chemistry ◽

10.1002/(sici)1096-987x(199603)17:4<409::aid-jcc3>3.0.co;2-y ◽

1996 ◽

Vol 17 (4) ◽

pp. 409-417 ◽

Cited By ~ 10

Author(s):

Michael Falk ◽

Peter F. Spierenburg ◽

John A. Walter

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Natural Products ◽

Magnetic Resonance ◽

Nuclear Magnetic Resonance Data ◽

Magnetic Resonance Data ◽

Resonance Data ◽

Nuclear Magnetic

Assessing and refining molecular dynamics simulations of proteins with nuclear magnetic resonance data

Biophysical Reviews ◽

10.1007/s12551-012-0087-6 ◽

2012 ◽

Vol 4 (3) ◽

pp. 189-203 ◽

Cited By ~ 7

Author(s):

Jane R. Allison

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Molecular Dynamics Simulations ◽

Nuclear Magnetic Resonance Data ◽

Magnetic Resonance Data ◽

Resonance Data ◽

Dynamics Simulations ◽

Nuclear Magnetic