Kozakov D - Search Results

1

ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT.

Porter KA, Xia B, Beglov D, Bohnuud T, Alam N, Schueler-Furman O, Kozakov D. Porter KA, et al. Among authors: kozakov d. Bioinformatics. 2017 Oct 15;33(20):3299-3301. doi: 10.1093/bioinformatics/btx216. Bioinformatics. 2017. PMID: 28430871 Free PMC article.

2

MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.

Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. Glukhov E, et al. Among authors: kozakov d. bioRxiv [Preprint]. 2023 Dec 14:2023.11.29.569310. doi: 10.1101/2023.11.29.569310. bioRxiv. 2023. Update in: Biophys J. 2024 Sep 3;123(17):2902-2909. doi: 10.1016/j.bpj.2024.05.011 PMID: 38077000 Free PMC article. Updated. Preprint.

3

PIPER: an FFT-based protein docking program with pairwise potentials.

Kozakov D, Brenke R, Comeau SR, Vajda S. Kozakov D, et al. Proteins. 2006 Nov 1;65(2):392-406. doi: 10.1002/prot.21117. Proteins. 2006. PMID: 16933295

4

Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI.

Shen Y, Brenke R, Kozakov D, Comeau SR, Beglov D, Vajda S. Shen Y, et al. Among authors: kozakov d. Proteins. 2007 Dec 1;69(4):734-42. doi: 10.1002/prot.21754. Proteins. 2007. PMID: 17853451

5

ClusPro: performance in CAPRI rounds 6-11 and the new server.

Comeau SR, Kozakov D, Brenke R, Shen Y, Beglov D, Vajda S. Comeau SR, et al. Among authors: kozakov d. Proteins. 2007 Dec 1;69(4):781-5. doi: 10.1002/prot.21795. Proteins. 2007. PMID: 17876812

6

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima.

Kozakov D, Schueler-Furman O, Vajda S. Kozakov D, et al. Proteins. 2008 Aug 15;72(3):993-1004. doi: 10.1002/prot.21997. Proteins. 2008. PMID: 18300245 Free PMC article.

7

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.

Ritchie DW, Kozakov D, Vajda S. Ritchie DW, et al. Among authors: kozakov d. Bioinformatics. 2008 Sep 1;24(17):1865-73. doi: 10.1093/bioinformatics/btn334. Epub 2008 Jun 30. Bioinformatics. 2008. PMID: 18591193 Free PMC article.

8

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques.

Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. Brenke R, et al. Among authors: kozakov d. Bioinformatics. 2009 Mar 1;25(5):621-7. doi: 10.1093/bioinformatics/btp036. Epub 2009 Jan 28. Bioinformatics. 2009. PMID: 19176554 Free PMC article.

9

Convergence and combination of methods in protein-protein docking.

Vajda S, Kozakov D. Vajda S, et al. Among authors: kozakov d. Curr Opin Struct Biol. 2009 Apr;19(2):164-70. doi: 10.1016/j.sbi.2009.02.008. Epub 2009 Mar 25. Curr Opin Struct Biol. 2009. PMID: 19327983 Free PMC article. Review.

10

Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors.

Beglov D, Lee CJ, De Biasio A, Kozakov D, Brenke R, Vajda S, Beglova N. Beglov D, et al. Among authors: kozakov d. Proteins. 2009 Dec;77(4):940-9. doi: 10.1002/prot.22519. Proteins. 2009. PMID: 19676115 Free PMC article.

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