Literature DB >> 17455371

Computational methods in protein structure prediction.

C A Floudas1.   

Abstract

This review presents the advances in protein structure prediction from the computational methods perspective. The approaches are classified into four major categories: comparative modeling, fold recognition, first principles methods that employ database information, and first principles methods without database information. Important advances along with current limitations and challenges are presented. (c) 2007 Wiley Periodicals, Inc.

Mesh:

Year:  2007        PMID: 17455371     DOI: 10.1002/bit.21411

Source DB:  PubMed          Journal:  Biotechnol Bioeng        ISSN: 0006-3592            Impact factor:   4.530


  38 in total

1.  Discovery of entry inhibitors for HIV-1 via a new de novo protein design framework.

Authors:  M L Bellows; M S Taylor; P A Cole; L Shen; R F Siliciano; H K Fung; C A Floudas
Journal:  Biophys J       Date:  2010-11-17       Impact factor: 4.033

2.  Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.

Authors:  Dong Xu; Jian Zhang; Ambrish Roy; Yang Zhang
Journal:  Proteins       Date:  2011-08-23

3.  An improved hybrid global optimization method for protein tertiary structure prediction.

Authors:  Scott R McAllister; Christodoulos A Floudas
Journal:  Comput Optim Appl       Date:  2010-03-01       Impact factor: 2.167

4.  Generalized pattern search algorithm for Peptide structure prediction.

Authors:  Giuseppe Nicosia; Giovanni Stracquadanio
Journal:  Biophys J       Date:  2008-05-16       Impact factor: 4.033

5.  Selecting high quality protein structures from diverse conformational ensembles.

Authors:  Ashwin Subramani; Peter A DiMaggio; Christodoulos A Floudas
Journal:  Biophys J       Date:  2009-09-16       Impact factor: 4.033

6.  An Improved Integration of Template-Based and Template-Free Protein Structure Modeling Methods and its Assessment in CASP11.

Authors:  Jilong Li; Badri Adhikari; Jianlin Cheng
Journal:  Protein Pept Lett       Date:  2015       Impact factor: 1.890

7.  Discovering free energy basins for macromolecular systems via guided multiscale simulation.

Authors:  Yuriy V Sereda; Abhishek B Singharoy; Martin F Jarrold; Peter J Ortoleva
Journal:  J Phys Chem B       Date:  2012-03-30       Impact factor: 2.991

8.  What is the best reference state for designing statistical atomic potentials in protein structure prediction?

Authors:  Haiyou Deng; Ya Jia; Yanyu Wei; Yang Zhang
Journal:  Proteins       Date:  2012-06-18

9.  Exploring the structure of the 100 amino-acid residue long N-terminus of the plant antenna protein CP29.

Authors:  Maryam Hashemi Shabestari; Cor J A M Wolfs; Ruud B Spruijt; Herbert van Amerongen; Martina Huber
Journal:  Biophys J       Date:  2014-03-18       Impact factor: 4.033

10.  Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences.

Authors:  Marcin J Mizianty; Lukasz Kurgan
Journal:  BMC Bioinformatics       Date:  2009-12-13       Impact factor: 3.169

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