Literature DB >> 19759849

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking.

Ioannis Ch Paschalidis1, Yang Shen, Pirooz Vakili, Sandor Vajda.   

Abstract

This paper introduces a new stochastic global optimization method targeting protein-protein docking problems, an important class of problems in computational structural biology. The method is based on finding general convex quadratic underestimators to the binding energy function that is funnel-like. Finding the optimum underestimator requires solving a semidefinite programming problem, hence the name semidefinite programming-based underestimation (SDU). The underestimator is used to bias sampling in the search region. It is established that under appropriate conditions SDU locates the global energy minimum with probability approaching one as the sample size grows. A detailed comparison of SDU with a related method of convex global underestimator (CGU), and computational results for protein-protein docking problems are provided.

Entities:  

Year:  2007        PMID： 19759849      PMCID： PMC2744142          DOI： 10.1109/TAC.2007.894518

Source DB:  PubMed          Journal:  IEEE Trans Automat Contr        ISSN： 0018-9286            Impact factor:   5.792


  7 in total

Review 1.  Folding funnels, binding funnels, and protein function.

Authors:  C J Tsai; S Kumar; B Ma; R Nussinov
Journal:  Protein Sci       Date:  1999-06       Impact factor: 6.725

2.  Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins.

Authors:  S Dennis; S Vajda
Journal:  J Comput Chem       Date:  2002-02       Impact factor: 3.376

3.  Protein docking along smooth association pathways.

Authors:  C J Camacho; S Vajda
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-21       Impact factor: 11.205

Review 4.  Principles of docking: An overview of search algorithms and a guide to scoring functions.

Authors:  Inbal Halperin; Buyong Ma; Haim Wolfson; Ruth Nussinov
Journal:  Proteins       Date:  2002-06-01

5.  ClusPro: an automated docking and discrimination method for the prediction of protein complexes.

Authors:  Stephen R Comeau; David W Gatchell; Sandor Vajda; Carlos J Camacho
Journal:  Bioinformatics       Date:  2004-01-01       Impact factor: 6.937

6.  Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.

Authors:  Jeffrey J Gray; Stewart Moughon; Chu Wang; Ora Schueler-Furman; Brian Kuhlman; Carol A Rohl; David Baker
Journal:  J Mol Biol       Date:  2003-08-01       Impact factor: 5.469

7.  Determination of atomic desolvation energies from the structures of crystallized proteins.

Authors:  C Zhang; G Vasmatzis; J L Cornette; C DeLisi
Journal:  J Mol Biol       Date:  1997-04-04       Impact factor: 5.469
  7 in total
  9 in total

1.  DARS (Decoys As the Reference State) potentials for protein-protein docking.

Authors:  Gwo-Yu Chuang; Dima Kozakov; Ryan Brenke; Stephen R Comeau; Sandor Vajda
Journal:  Biophys J       Date:  2008-08-01       Impact factor: 4.033

Review 2.  Convergence and combination of methods in protein-protein docking.

Authors:  Sandor Vajda; Dima Kozakov
Journal:  Curr Opin Struct Biol       Date:  2009-03-25       Impact factor: 6.809

3.  A New Approach to Rigid Body Minimization with Application to Molecular Docking.

Authors:  Hanieh Mirzaei; Dima Kozakov; Dmitri Beglov; Ioannis Ch Paschalidis; Sandor Vajda; Pirooz Vakili
Journal:  Proc IEEE Conf Decis Control       Date:  2012-12

4.  Energy Minimization on Manifolds for Docking Flexible Molecules.

Authors:  Hanieh Mirzaei; Shahrooz Zarbafian; Elizabeth Villar; Scott Mottarella; Dmitri Beglov; Sandor Vajda; Ioannis Ch Paschalidis; Pirooz Vakili; Dima Kozakov
Journal:  J Chem Theory Comput       Date:  2015-03-10       Impact factor: 6.006

5.  Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach.

Authors:  Pirooz Vakili; Hanieh Mirzaei; Shahrooz Zarbafian; Ioannis Ch Paschalidis; Dima Kozakov; Sandor Vajda
Journal:  Proc IEEE Conf Decis Control       Date:  2014-12

6.  A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking.

Authors:  Feng Nan; Mohammad Moghadasi; Pirooz Vakili; Sandor Vajda; Dima Kozakov; Ioannis Ch Paschalidis
Journal:  Proc IEEE Conf Decis Control       Date:  2014-12

7.  A Message Passing Approach to Side Chain Positioning with Applications in Protein Docking Refinement.

Authors:  Mohammad Moghadasi; Dima Kozakov; Artem B Mamonov; Pirooz Vakili; Sandor Vajda; Ioannis Ch Paschalidis
Journal:  Proc IEEE Conf Decis Control       Date:  2012

8.  Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes.

Authors:  Shahrooz Zarbafian; Mohammad Moghadasi; Athar Roshandelpoor; Feng Nan; Keyong Li; Pirooz Vakli; Sandor Vajda; Dima Kozakov; Ioannis Ch Paschalidis
Journal:  Sci Rep       Date:  2018-04-12       Impact factor: 4.379

9.  Protein docking by the underestimation of free energy funnels in the space of encounter complexes.

Authors:  Yang Shen; Ioannis Ch Paschalidis; Pirooz Vakili; Sandor Vajda
Journal:  PLoS Comput Biol       Date:  2008-10-10       Impact factor: 4.475
  9 in total

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