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Items: 17

1.

Focused grid-based resampling for protein docking and mapping.

Mamonov AB, Moghadasi M, Mirzaei H, Zarbafian S, Grove LE, Bohnuud T, Vakili P, Ch Paschalidis I, Vajda S, Kozakov D.

J Comput Chem. 2016 Apr 30;37(11):961-70. doi: 10.1002/jcc.24273. Epub 2016 Feb 2.

2.

Energy Minimization on Manifolds for Docking Flexible Molecules.

Mirzaei H, Zarbafian S, Villar E, Mottarella S, Beglov D, Vajda S, Paschalidis ICh, Vakili P, Kozakov D.

J Chem Theory Comput. 2015 Mar 10;11(3):1063-76.

3.

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

Nan F, Moghadasi M, Vakili P, Vajda S, Kozakov D, Ch Paschalidis I.

Proc IEEE Conf Decis Control. 2014 Dec;2014:4623-4628.

4.

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

Vakili P, Mirzaei H, Zarbafian S, Paschalidis IC, Kozakov D, Vajda S.

Proc IEEE Conf Decis Control. 2014 Dec;2014:5825-5830.

5.

The impact of side-chain packing on protein docking refinement.

Moghadasi M, Mirzaei H, Mamonov A, Vakili P, Vajda S, Paschalidis ICh, Kozakov D.

J Chem Inf Model. 2015 Apr 27;55(4):872-81. doi: 10.1021/ci500380a. Epub 2015 Mar 24.

6.

Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations.

Chowdhury R, Beglov D, Moghadasi M, Paschalidis IC, Vakili P, Vajda S, Bajaj C, Kozakov D.

J Chem Theory Comput. 2014 Oct 14;10(10):4449-4454. Epub 2014 Sep 5.

7.

Encounter complexes and dimensionality reduction in protein-protein association.

Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, Schueler-Furman O, Paschalidis ICh, Clore GM, Vajda S.

Elife. 2014 Apr 8;3:e01370. doi: 10.7554/eLife.01370.

8.

Modulation of synaptic function through the α-neurexin-specific ligand neurexophilin-1.

Born G, Breuer D, Wang S, Rohlmann A, Coulon P, Vakili P, Reissner C, Kiefer F, Heine M, Pape HC, Missler M.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):E1274-83. doi: 10.1073/pnas.1312112111. Epub 2014 Mar 17.

9.

Rigid Body Energy Minimization on Manifolds for Molecular Docking.

Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D.

J Chem Theory Comput. 2012 Nov 13;8(11):4374-4380. Epub 2012 Aug 21.

10.

A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein Docking*

Moghadasi M, Kozakov D, Vakili P, Vajda S, Paschalidis IC.

Proc IEEE Conf Decis Control. 2013:739-744.

11.

Flexible Refinement of Protein-Ligand Docking on Manifolds.

Mirzaei H, Villar E, Mottarella S, Beglov D, Paschalidis IC, Vajda S, Kozakov D, Vakili P.

Proc IEEE Conf Decis Control. 2013:1392-1397.

12.

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

Mirzaei H, Kozakov D, Beglov D, Paschalidis IC, Vajda S, Vakili P.

Proc IEEE Conf Decis Control. 2012 Dec:2983-2988.

13.

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

Moghadasi M, Kozakov D, Mamonov AB, Vakili P, Vajda S, Paschalidis IC.

Proc IEEE Conf Decis Control. 2012:2310-2315.

14.

Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19.

Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR, Shen Y, Li K, Zheng J, Vakili P, Paschalidis ICh, Vajda S.

Proteins. 2010 Nov 15;78(15):3124-30. doi: 10.1002/prot.22835.

15.

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

Shen Y, Paschalidis ICh, Vakili P, Vajda S.

PLoS Comput Biol. 2008 Oct;4(10):e1000191. doi: 10.1371/journal.pcbi.1000191. Epub 2008 Oct 10.

16.

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.

Paschalidis ICh, Shen Y, Vakili P, Vajda S.

Conf Proc IEEE Eng Med Biol Soc. 2006;2006:5330-3.

17.

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

Paschalidis IC, Shen Y, Vakili P, Vajda S.

IEEE Trans Automat Contr. 2007 Apr 1;52(4):664-676.

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