Literature DB >> 16364908

Protein structure prediction: inroads to biology.

Donald Petrey1, Barry Honig.   

Abstract

In recent years, there has been significant progress in the ability to predict the three-dimensional structure of proteins from their amino acid sequence. Progress has been due to new methods to extract the growing amount of information in sequence and structure databases and improved computational descriptions of protein energetics. This review summarizes recent advances in these areas and describes a number of novel biological applications made possible by structure prediction. Despite remaining challenges, protein structure prediction is becoming an extremely useful tool in understanding phenomena in modern molecular and cell biology.

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Year:  2005        PMID: 16364908     DOI: 10.1016/j.molcel.2005.12.005

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  54 in total

1.  Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking.

Authors:  Pandian Sokkar; Shylajanaciyar Mohandass; Murugesan Ramachandran
Journal:  J Mol Model       Date:  2010-10-06       Impact factor: 1.810

2.  Ion mobility mass spectrometry coupled with rapid protein threading predictor structure prediction and collision-induced dissociation for probing chemokine conformation and stability.

Authors:  Milady R Niñonuevo; Julie A Leary
Journal:  Anal Chem       Date:  2012-03-16       Impact factor: 6.986

Review 3.  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

4.  On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins.

Authors:  Lucy R Forrest; Christopher L Tang; Barry Honig
Journal:  Biophys J       Date:  2006-04-28       Impact factor: 4.033

5.  Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

Authors:  Adam Liwo; Mey Khalili; Cezary Czaplewski; Sebastian Kalinowski; Staniłsaw Ołdziej; Katarzyna Wachucik; Harold A Scheraga
Journal:  J Phys Chem B       Date:  2007-01-11       Impact factor: 2.991

6.  Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid.

Authors:  Michael T Woodside; Peter C Anthony; William M Behnke-Parks; Kevan Larizadeh; Daniel Herschlag; Steven M Block
Journal:  Science       Date:  2006-11-10       Impact factor: 47.728

Review 7.  Membrane protein prediction methods.

Authors:  Marco Punta; Lucy R Forrest; Henry Bigelow; Andrew Kernytsky; Jinfeng Liu; Burkhard Rost
Journal:  Methods       Date:  2007-04       Impact factor: 3.608

8.  Fold assessment for comparative protein structure modeling.

Authors:  Francisco Melo; Andrej Sali
Journal:  Protein Sci       Date:  2007-09-28       Impact factor: 6.725

9.  Local quality assessment in homology models using statistical potentials and support vector machines.

Authors:  Marc Fasnacht; Jiang Zhu; Barry Honig
Journal:  Protein Sci       Date:  2007-06-28       Impact factor: 6.725

10.  Identification of a chloride ion binding site in Na+/Cl -dependent transporters.

Authors:  Lucy R Forrest; Sotiria Tavoulari; Yuan-Wei Zhang; Gary Rudnick; Barry Honig
Journal:  Proc Natl Acad Sci U S A       Date:  2007-07-24       Impact factor: 11.205

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