Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three-dimensional structure of murine homeodomain Msx-1

Haicheng Li; Roberto Tejero; Daniel Monleon; Donna Bassolino-Klimas; Cory Abate-Shen; Robert E. Bruccoleri; Gaetano T. Montelione

doi:10.1002/pro.5560060502

Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three-dimensional structure of murine homeodomain Msx-1

Protein Science ◽

10.1002/pro.5560060502 ◽

1997 ◽

Vol 6 (5) ◽

pp. 956-970 ◽

Cited By ~ 29

Author(s):

Haicheng Li ◽

Roberto Tejero ◽

Daniel Monleon ◽

Donna Bassolino-Klimas ◽

Cory Abate-Shen ◽

...

Keyword(s):

Molecular Dynamics ◽

Simulated Annealing ◽

Homology Modeling ◽

Three Dimensional ◽

Conformational Search ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Restrained Molecular Dynamics

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Three-dimensional structure of the complexes of ribonuclease A with 2′,5′-CpA and 3′,5′-d(CpA) in aqueous solution, as obtained by NMR and restrained molecular dynamics

Protein Science ◽

10.1002/pro.5560050817 ◽

1996 ◽

Vol 5 (8) ◽

pp. 1633-1647 ◽

Cited By ~ 21

Author(s):

Catherine Toiron ◽

Carlos Gonzalez ◽

Marta Bruix ◽

Manuel Rico

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Three Dimensional ◽

Ribonuclease A ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Restrained Molecular Dynamics

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The three-dimensional structure of α1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics

The EMBO Journal ◽

10.1002/j.1460-2075.1986.tb04557.x ◽

1986 ◽

Vol 5 (10) ◽

pp. 2729-2735 ◽

Cited By ~ 186

Author(s):

G. Marius Clore ◽

Michael Nilges ◽

Dinesh K. Sukumaran ◽

Axel T. Brünger ◽

Martin Karplus ◽

...

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Distance Geometry ◽

Three Dimensional ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Combined Use ◽

Restrained Molecular Dynamics ◽

Nuclear Magnetic

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A three-dimensional structure of Plasmodium falciparum serine hydroxymethyltransferase in complex with glycine and 5-formyl-tetrahydrofolate. Homology modeling and molecular dynamics

Biophysical Chemistry ◽

10.1016/j.bpc.2004.12.002 ◽

2005 ◽

Vol 115 (1) ◽

pp. 1-10 ◽

Cited By ~ 23

Author(s):

Tanos C.C. França ◽

Pedro G. Pascutti ◽

Teodorico C. Ramalho ◽

Jose´ D. Figueroa-Villar

Keyword(s):

Molecular Dynamics ◽

Plasmodium Falciparum ◽

Homology Modeling ◽

Three Dimensional ◽

Serine Hydroxymethyltransferase ◽

Dimensional Structure ◽

Three Dimensional Structure

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The three-dimensional structure in solution (pH 5.8) of a DNA 9-mer duplex containing 1,N2-propanodeoxyguanosine opposite deoxyadenosine. Restrained molecular dynamics and NOE-based refinement calculations

Biochemistry ◽

10.1021/bi00143a023 ◽

1992 ◽

Vol 31 (28) ◽

pp. 6518-6532 ◽

Cited By ~ 13

Author(s):

Ping Huang ◽

Moises Eisenberg

Keyword(s):

Molecular Dynamics ◽

Three Dimensional ◽

Dimensional Structure ◽

Solution Ph ◽

Three Dimensional Structure ◽

Structure In Solution ◽

Restrained Molecular Dynamics

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Three-Dimensional Structure of RNA Monomeric G-Quadruplex Containing ALS and FTD Related G4C2 Repeat and Its Binding with TMPyP4 Probed by Homology Modeling based on Experimental Constraints and Molecular Dynamics Simulations

ACS Chemical Neuroscience ◽

10.1021/acschemneuro.9b00572 ◽

2019 ◽

Vol 11 (1) ◽

pp. 57-75 ◽

Cited By ~ 3

Author(s):

Kelly Mulholland ◽

Holli-Joi Sullivan ◽

Joseph Garner ◽

Jun Cai ◽

Brian Chen ◽

...

Keyword(s):

Molecular Dynamics ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Three Dimensional ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

G Quadruplex ◽

Dynamics Simulations

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Three-dimensional structure of phoratoxin in solution: combined use of nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

Biochemistry ◽

10.1021/bi00380a037 ◽

1987 ◽

Vol 26 (6) ◽

pp. 1732-1745 ◽

Cited By ~ 58

Author(s):

G. Marius Clore ◽

Dinesh K. Sukumaran ◽

Michael Nilges ◽

Angela M. Gronenborn

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Distance Geometry ◽

Three Dimensional ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Combined Use ◽

Restrained Molecular Dynamics ◽

Nuclear Magnetic

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Use of restrained molecular dynamics in water to determine three-dimensional protein structure: Prediction of the three-dimensional structure ofEcballium elaterium trypsin inhibitor II

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.340060407 ◽

1989 ◽

Vol 6 (4) ◽

pp. 405-417 ◽

Cited By ~ 48

Author(s):

Laurent Chiche ◽

Christine Gaboriaud ◽

Annie Heitz ◽

Jean-Paul Mornon ◽

Bertrand Castro ◽

...

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Protein Structure Prediction ◽

Trypsin Inhibitor ◽

Structure Prediction ◽

Three Dimensional ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Restrained Molecular Dynamics

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Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

Biochemistry ◽

10.1021/bi00398a069 ◽

1987 ◽

Vol 26 (24) ◽

pp. 8012-8023 ◽

Cited By ~ 202

Author(s):

G. Marius Clore ◽

Angela M. Gronenborn ◽

Michael Nilges ◽

Clarence A. Ryan

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Distance Geometry ◽

Three Dimensional ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Carboxypeptidase Inhibitor ◽

Restrained Molecular Dynamics ◽

Nuclear Magnetic

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Three-Dimensional Structure of Cyclohexapeptides Containing a Phosphinic Bond in Aqueous Solution: A Template for Zinc Metalloprotease Inhibitors. A NMR And Restrained Molecular Dynamics Study

Journal of Medicinal Chemistry ◽

10.1021/jm00003a018 ◽

1995 ◽

Vol 38 (3) ◽

pp. 553-564 ◽

Cited By ~ 2

Author(s):

Philippe Cuniasse ◽

Isabelle Raynal ◽

Alain Lecoq ◽

Anasthasios Yiotakis ◽

Vincent Dive

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Three Dimensional ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Zinc Metalloprotease ◽

Metalloprotease Inhibitors ◽

Restrained Molecular Dynamics

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Three-dimensional structure of HIV-1 VIF constructed by comparative modeling and the function characterization analyzed by molecular dynamics simulation

Organic & Biomolecular Chemistry ◽

10.1039/b612050d ◽

2007 ◽

Vol 5 (4) ◽

pp. 617 ◽

Cited By ~ 21

Author(s):

Wei Lv ◽

Zhenming Liu ◽

Hongwei Jin ◽

Xianghui Yu ◽

Liangren Zhang ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Three Dimensional ◽

Comparative Modeling ◽

Dynamics Simulation ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Function Characterization ◽

Hiv 1

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