Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations

Kirsi Tappura

doi:10.1002/prot.1082

Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.1082 ◽

2001 ◽

Vol 44 (3) ◽

pp. 167-179 ◽

Cited By ~ 14

Author(s):

Kirsi Tappura

Keyword(s):

Molecular Dynamics ◽

Rotational Energy ◽

Conformational Search ◽

Energy Barriers ◽

Protein Loops

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Conformations of Lower-Size Large Cyclodextrins (DP from 10 to 30) Derived from Conformational Search with Molecular Dynamics and Principal Component Analysis

Current Physical Chemistrye ◽

10.2174/1877947611202040413 ◽

2012 ◽

Vol 2 (4) ◽

pp. 413-442

Author(s):

Petko Ivanov

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Principal Component ◽

Component Analysis ◽

Conformational Search ◽

Lower Size

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Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search

The Journal of Physical Chemistry B ◽

10.1021/jp9817372 ◽

1998 ◽

Vol 102 (37) ◽

pp. 7238-7250 ◽

Cited By ~ 77

Author(s):

Xiongwu Wu ◽

Shaomeng Wang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Conformational Search

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Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct200615k ◽

2011 ◽

Vol 8 (1) ◽

pp. 17-23 ◽

Cited By ~ 25

Author(s):

William Sinko ◽

César Augusto F. de Oliveira ◽

Levi C. T. Pierce ◽

J. Andrew McCammon

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

High Energy ◽

Energy Barriers ◽

Accelerated Molecular Dynamics ◽

New Equation ◽

Dynamics Simulations

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Energy directed conformational search of protein loops and segments

Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding - DIMACS Series in Discrete Mathematics and Theoretical Computer Science ◽

10.1090/dimacs/023/02 ◽

1995 ◽

pp. 15-28

Author(s):

Robert Bruccoleri

Keyword(s):

Conformational Search ◽

Protein Loops

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Conformational Search on the Tripeptides Structure by Molecular Dynamics: Study of L,L-Gly-Phe-Phe, L,L-Phe-Gly-Phe, and L,L-Phe-Phe-Gly

Drug Designing Open Access ◽

10.4172/2169-0138.1000106 ◽

2013 ◽

Vol 02 (02) ◽

Author(s):

Khebichat N Nekkaz K

Keyword(s):

Molecular Dynamics ◽

Conformational Search

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Computer simulations of cyclic and acyclic cholinergic agonists: conformational search and molecular dynamics simulations

Biophysical Journal ◽

10.1016/s0006-3495(94)80780-5 ◽

1994 ◽

Vol 66 (2) ◽

pp. 314-324 ◽

Cited By ~ 1

Author(s):

K.A. McGroddy ◽

J.W. Brady ◽

R.E. Oswald

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Computer Simulations ◽

Conformational Search ◽

Cholinergic Agonists ◽

Dynamics Simulations

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Distance geometry and molecular dynamics conformational search of a cyclic peptide for proteinde novodesign

Acta Crystallographica Section A Foundations of Crystallography ◽

10.1107/s0108767378095677 ◽

1993 ◽

Vol 49 (s1) ◽

pp. c151-c152

Author(s):

Z.-W. Luo ◽

L.-H. Lai ◽

X.-J. Xu

Keyword(s):

Molecular Dynamics ◽

Cyclic Peptide ◽

Distance Geometry ◽

Conformational Search

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Computational studies on FK506: conformational search and molecular dynamics simulation in water

Journal of the American Chemical Society ◽

10.1021/ja00025a010 ◽

1991 ◽

Vol 113 (25) ◽

pp. 9483-9493 ◽

Cited By ~ 13

Author(s):

Julianto Pranata ◽

William L. Jorgensen

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Conformational Search ◽

Computational Studies

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ChemInform Abstract: Computational Studies on FK506: Conformational Search and Molecular Dynamics Simulation in Water.

ChemInform ◽

10.1002/chin.199213064 ◽

2010 ◽

Vol 23 (13) ◽

pp. no-no

Author(s):

J. PRANATA ◽

W. L. JORGENSEN

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Conformational Search ◽

Computational Studies

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Potential-scaled molecular dynamics and potential annealing: effective conformational search techniques for biomolecules

The Journal of Physical Chemistry ◽

10.1021/j100119a028 ◽

1993 ◽

Vol 97 (17) ◽

pp. 4416-4420 ◽

Cited By ~ 27

Author(s):

Hideki Tsujishita ◽

Ikuo Moriguchi ◽

Shuichi Hirono

Keyword(s):

Molecular Dynamics ◽

Conformational Search ◽

Search Techniques

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