A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field

M. Chinchio; C. Czaplewski; S. Ołdziej; H. A. Scheraga

doi:10.1137/060649318

A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field

Multiscale Modeling and Simulation ◽

10.1137/060649318 ◽

2006 ◽

Vol 5 (4) ◽

pp. 1175-1195 ◽

Cited By ~ 4

Author(s):

M. Chinchio ◽

C. Czaplewski ◽

S. Ołdziej ◽

H. A. Scheraga

Keyword(s):

Protein Structure ◽

Force Field ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Multiscale Approach ◽

Low Resolution ◽

Hierarchical Multiscale

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Genetic Algorithm inAb Initio Protein Structure Prediction Using Low Resolution Model: A Review

Biomedical Data and Applications - Studies in Computational Intelligence ◽

10.1007/978-3-642-02193-0_14 ◽

2009 ◽

pp. 317-342 ◽

Cited By ~ 17

Author(s):

Md. Tamjidul Hoque ◽

Madhu Chetty ◽

Abdul Sattar

Keyword(s):

Genetic Algorithm ◽

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Low Resolution ◽

Resolution Model

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Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems†

The Journal of Physical Chemistry B ◽

10.1021/jp030844f ◽

2004 ◽

Vol 108 (27) ◽

pp. 9421-9438 ◽

Cited By ~ 88

Author(s):

Adam Liwo ◽

Stanisław Ołdziej ◽

Cezary Czaplewski ◽

Urszula Kozłowska ◽

Harold A. Scheraga

Keyword(s):

Protein Structure ◽

Force Field ◽

Ab Initio ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Model Systems ◽

Energy Surfaces

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Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field

BMC Structural Biology ◽

10.1186/1472-6807-7-43 ◽

2007 ◽

Vol 7 (1) ◽

pp. 43 ◽

Cited By ~ 37

Author(s):

Sebastian Kmiecik ◽

Dominik Gront ◽

Andrzej Kolinski

Keyword(s):

Protein Structure ◽

High Resolution ◽

Force Field ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Reduced Models

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MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein–Protein Network Mapping

Journal of Molecular Biology ◽

10.1016/j.jmb.2018.03.004 ◽

2018 ◽

Vol 430 (15) ◽

pp. 2256-2265 ◽

Cited By ~ 19

Author(s):

Chengxin Zhang ◽

Wei Zheng ◽

Peter L. Freddolino ◽

Yang Zhang

Keyword(s):

Gene Ontology ◽

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Protein Network ◽

Low Resolution ◽

Homologous Proteins ◽

Network Mapping

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Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20133 ◽

2004 ◽

Vol 56 (3) ◽

pp. 475-486 ◽

Cited By ~ 40

Author(s):

Meng-Juei Hsieh ◽

Ray Luo

Keyword(s):

Protein Structure ◽

Force Field ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Scoring Function ◽

Implicit Solvent ◽

Amber Force Field ◽

Poisson Boltzmann

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Protein Structure Prediction with a Combined Solvation Free Energy-Molecular Mechanics Force Field

Molecular Simulation ◽

10.1080/08927029308022162 ◽

1993 ◽

Vol 10 (2-6) ◽

pp. 121-149 ◽

Cited By ~ 57

Author(s):

Celia A. Schiffer ◽

James W. Caldwell ◽

Peter A. Kollman ◽

Robert M. Stroud

Keyword(s):

Free Energy ◽

Protein Structure ◽

Force Field ◽

Molecular Mechanics ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Solvation Free Energy

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A Fast Algorithm for Low-Resolution Protein Structure Prediction

2006 International Conference of the IEEE Engineering in Medicine and Biology Society ◽

10.1109/iembs.2006.259358 ◽

2006 ◽

Cited By ~ 3

Author(s):

Rajkumar Bondugula ◽

Dong Xu ◽

Yi Shang

Keyword(s):

Protein Structure ◽

Protein Structure Prediction ◽

Fast Algorithm ◽

Structure Prediction ◽

Low Resolution

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Multimodal Memetic Framework for low-resolution protein structure prediction

Swarm and Evolutionary Computation ◽

10.1016/j.swevo.2019.100608 ◽

2020 ◽

Vol 52 ◽

pp. 100608 ◽

Cited By ~ 3

Author(s):

Rumana Nazmul ◽

Madhu Chetty ◽

Ahsan Raja Chowdhury

Keyword(s):

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Low Resolution

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Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation

Journal of Computational Chemistry ◽

10.1002/jcc.20963 ◽

2008 ◽

Vol 29 (12) ◽

pp. 1930-1944 ◽

Cited By ~ 7

Author(s):

Daisuke Katagiri ◽

Hideyoshi Fuji ◽

Saburo Neya ◽

Tyuji Hoshino

Keyword(s):

Protein Structure ◽

Force Field ◽

Ab Initio ◽

Protein Structure Prediction ◽

Quantum Chemical Calculation ◽

Quantum Chemical ◽

Structure Prediction ◽

Water Phase ◽

Chemical Calculation ◽

Force Field Parameters

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A Fast Algorithm for Low-Resolution Protein Structure Prediction

2006 International Conference of the IEEE Engineering in Medicine and Biology Society ◽

10.1109/iembs.2006.4398782 ◽

2006 ◽

Cited By ~ 1

Author(s):

Rajkumar Bondugula ◽

Dong Xu ◽

Yi Shang

Keyword(s):

Protein Structure ◽

Protein Structure Prediction ◽

Fast Algorithm ◽

Structure Prediction ◽

Low Resolution

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