Literature DB >> 25774073

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

Pirooz Vakili1, Hanieh Mirzaei2, Shahrooz Zarbafian3, Ioannis Ch Paschalidis4, Dima Kozakov5, Sandor Vajda5.   

Abstract

In this paper we consider the problem of minimization of a cost function that depends on the location and poses of one or more rigid bodies, or bodies that consist of rigid parts hinged together. We present a unified setting for formulating this problem as an optimization on an appropriately defined manifold for which efficient manifold optimizations can be developed. This setting is based on a Lie group representation of the rigid movements of a body that is different from what is commonly used for this purpose. We illustrate this approach by using the steepest descent algorithm on the manifold of the search space and specify conditions for its convergence.

Entities:  

Year:  2014        PMID: 25774073      PMCID: PMC4357846          DOI: 10.1109/CDC.2014.7040301

Source DB:  PubMed          Journal:  Proc IEEE Conf Decis Control        ISSN: 0743-1546


  6 in total

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

Authors:  Ioannis Ch Paschalidis; Yang Shen; Pirooz Vakili; Sandor Vajda
Journal:  IEEE Trans Automat Contr       Date:  2007-04-01       Impact factor: 5.792

2.  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

3.  Least-squares fitting of two 3-d point sets.

Authors:  K S Arun; T S Huang; S D Blostein
Journal:  IEEE Trans Pattern Anal Mach Intell       Date:  1987-05       Impact factor: 6.226

Review 4.  Group theory and biomolecular conformation: I. Mathematical and computational models.

Authors:  Gregory S Chirikjian
Journal:  J Phys Condens Matter       Date:  2010-08-18       Impact factor: 2.333

5.  Rigid Body Energy Minimization on Manifolds for Molecular Docking.

Authors:  Hanieh Mirzaei; Dmitri Beglov; Ioannis Ch Paschalidis; Sandor Vajda; Pirooz Vakili; Dima Kozakov
Journal:  J Chem Theory Comput       Date:  2012-08-21       Impact factor: 6.006

6.  Flexible Refinement of Protein-Ligand Docking on Manifolds.

Authors:  Hanieh Mirzaei; Elizabeth Villar; Scott Mottarella; Dmitri Beglov; Ioannis Ch Paschalidis; Sandor Vajda; Dima Kozakov; Pirooz Vakili
Journal:  Proc IEEE Conf Decis Control       Date:  2013
  6 in total

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