Literature DB >> 19100336

Protein structure prediction and model quality assessment.

Andriy Kryshtafovych1, Krzysztof Fidelis.   

Abstract

Protein structures have proven to be a crucial piece of information for biomedical research. Of the millions of currently sequenced proteins only a small fraction is experimentally solved for structure and the only feasible way to bridge the gap between sequence and structure data is computational modeling. Half a century has passed since it was shown that the amino acid sequence of a protein determines its shape, but a method to translate the sequence code reliably into the 3D structure still remains to be developed. This review summarizes modern protein structure prediction techniques with the emphasis on comparative modeling, and describes the recent advances in methods for theoretical model quality assessment.

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Year:  2009        PMID: 19100336      PMCID: PMC2808711          DOI: 10.1016/j.drudis.2008.11.010

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  60 in total

1.  Progress from CASP6 to CASP7.

Authors:  Andriy Kryshtafovych; Krzysztof Fidelis; John Moult
Journal:  Proteins       Date:  2007

2.  Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.

Authors:  Rhiju Das; Bin Qian; Srivatsan Raman; Robert Vernon; James Thompson; Philip Bradley; Sagar Khare; Michael D Tyka; Divya Bhat; Dylan Chivian; David E Kim; William H Sheffler; Lars Malmström; Andrew M Wollacott; Chu Wang; Ingemar Andre; David Baker
Journal:  Proteins       Date:  2007

3.  Automated server predictions in CASP7.

Authors:  James N D Battey; Jürgen Kopp; Lorenza Bordoli; Randy J Read; Neil D Clarke; Torsten Schwede
Journal:  Proteins       Date:  2007

4.  Assessment of CASP7 predictions for template-based modeling targets.

Authors:  Jürgen Kopp; Lorenza Bordoli; James N D Battey; Florian Kiefer; Torsten Schwede
Journal:  Proteins       Date:  2007

5.  Template-based modeling and free modeling by I-TASSER in CASP7.

Authors:  Yang Zhang
Journal:  Proteins       Date:  2007

6.  Assessing model accuracy using the homology modeling automatically software.

Authors:  Aneerban Bhattacharya; Zeba Wunderlich; Daniel Monleon; Roberto Tejero; Gaetano T Montelione
Journal:  Proteins       Date:  2008-01-01

7.  Comparative modeling in structural genomics.

Authors:  John Moult
Journal:  Structure       Date:  2008-01       Impact factor: 5.006

8.  Protein structure modeling with MODELLER.

Authors:  Narayanan Eswar; David Eramian; Ben Webb; Min-Yi Shen; Andrej Sali
Journal:  Methods Mol Biol       Date:  2008

9.  The assessment of methods for protein structure prediction.

Authors:  Anna Tramontano; Domenico Cozzetto; Alejandro Giorgetti; Domenico Raimondo
Journal:  Methods Mol Biol       Date:  2008

10.  Critical assessment of methods of protein structure prediction-Round VII.

Authors:  John Moult; Krzysztof Fidelis; Andriy Kryshtafovych; Burkhard Rost; Tim Hubbard; Anna Tramontano
Journal:  Proteins       Date:  2007
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  24 in total

1.  Distributions of experimental protein structures on coarse-grained free energy landscapes.

Authors:  Kannan Sankar; Jie Liu; Yuan Wang; Robert L Jernigan
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

Review 2.  Computational tools for epitope vaccine design and evaluation.

Authors:  Linling He; Jiang Zhu
Journal:  Curr Opin Virol       Date:  2015-03-31       Impact factor: 7.090

3.  FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level.

Authors:  Michal Brylinski; Jeffrey Skolnick
Journal:  Proteins       Date:  2010-12-06

4.  Probabilistic divergence of a template-based modelling methodology from the ideal protocol.

Authors:  Ashish Runthala
Journal:  J Mol Model       Date:  2021-01-07       Impact factor: 1.810

5.  Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.

Authors:  Michael T Zimmermann; Sumudu P Leelananda; Pawel Gniewek; Yaping Feng; Robert L Jernigan; Andrzej Kloczkowski
Journal:  J Struct Funct Genomics       Date:  2011-06-15

6.  Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models.

Authors:  Pawel Gniewek; Sumudu P Leelananda; Andrzej Kolinski; Robert L Jernigan; Andrzej Kloczkowski
Journal:  Proteins       Date:  2011-04-19

7.  A comparison of different functions for predicted protein model quality assessment.

Authors:  Juan Li; Huisheng Fang
Journal:  J Comput Aided Mol Des       Date:  2016-08-03       Impact factor: 3.686

8.  Investigating Molecular Mechanisms of Activation and Mutation of the HER2 Receptor Tyrosine Kinase through Computational Modeling and Simulation.

Authors:  Shannon E Telesco; Andrew Shih; Yingting Liu; Ravi Radhakrishnan
Journal:  Cancer Res J       Date:  2011

9.  Inhibition of the class C beta-lactamase from Acinetobacter spp.: insights into effective inhibitor design.

Authors:  Sarah M Drawz; Maja Babic; Christopher R Bethel; Magda Taracila; Anne M Distler; Claudia Ori; Emilia Caselli; Fabio Prati; Robert A Bonomo
Journal:  Biochemistry       Date:  2010-01-19       Impact factor: 3.162

Review 10.  Template-based protein modeling: recent methodological advances.

Authors:  Pankaj R Daga; Ronak Y Patel; Robert J Doerksen
Journal:  Curr Top Med Chem       Date:  2010       Impact factor: 3.295

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