Paschalidis ICh - Search Results

1

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. Kozakov D, et al. Among authors: paschalidis ich. Elife. 2014 Apr 8;3:e01370. doi: 10.7554/eLife.01370. Elife. 2014. PMID: 24714491 Free PMC article.

2

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

Paschalidis ICh, Shen Y, Vakili P, Vajda S. Paschalidis ICh, et al. Conf Proc IEEE Eng Med Biol Soc. 2006;2006:5330-3. doi: 10.1109/IEMBS.2006.260790. Conf Proc IEEE Eng Med Biol Soc. 2006. PMID: 17946298 Free PMC article.

3

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

Shen Y, Paschalidis ICh, Vakili P, Vajda S. Shen Y, et al. Among authors: paschalidis ich. PLoS Comput Biol. 2008 Oct;4(10):e1000191. doi: 10.1371/journal.pcbi.1000191. Epub 2008 Oct 10. PLoS Comput Biol. 2008. PMID: 18846200 Free PMC article.

4

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

Paschalidis IC, Shen Y, Vakili P, Vajda S. Paschalidis IC, et al. IEEE Trans Automat Contr. 2007 Apr 1;52(4):664-676. doi: 10.1109/TAC.2007.894518. IEEE Trans Automat Contr. 2007. PMID: 19759849 Free PMC article.

5

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. Kozakov D, et al. Among authors: paschalidis ich. Proteins. 2010 Nov 15;78(15):3124-30. doi: 10.1002/prot.22835. Proteins. 2010. PMID: 20818657 Free PMC article.

6

Rigid Body Energy Minimization on Manifolds for Molecular Docking.

Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D. Mirzaei H, et al. J Chem Theory Comput. 2012 Nov 13;8(11):4374-4380. doi: 10.1021/ct300272j. Epub 2012 Aug 21. J Chem Theory Comput. 2012. PMID: 23382659 Free PMC article.

7

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. Moghadasi M, et al. Proc IEEE Conf Decis Control. 2012:2310-2315. doi: 10.1109/cdc.2012.6426600. Proc IEEE Conf Decis Control. 2012. PMID: 23515575 Free PMC article.

8

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

Mirzaei H, Kozakov D, Beglov D, Paschalidis IC, Vajda S, Vakili P. Mirzaei H, et al. Proc IEEE Conf Decis Control. 2012 Dec:2983-2988. doi: 10.1109/CDC.2012.6426267. Proc IEEE Conf Decis Control. 2012. PMID: 24763338 Free PMC article.

9

Flexible Refinement of Protein-Ligand Docking on Manifolds.

Mirzaei H, Villar E, Mottarella S, Beglov D, Paschalidis IC, Vajda S, Kozakov D, Vakili P. Mirzaei H, et al. Proc IEEE Conf Decis Control. 2013:1392-1397. doi: 10.1109/CDC.2013.6760077. Proc IEEE Conf Decis Control. 2013. PMID: 24830567 Free PMC article.

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. Moghadasi M, et al. Proc IEEE Conf Decis Control. 2013:739-744. doi: 10.1109/CDC.2013.6759970. Proc IEEE Conf Decis Control. 2013. PMID: 24844567 Free PMC article.

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