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Results: 1 to 20 of 240

1.

GS-align for glycan structure alignment and similarity measurement.

Lee HS, Jo S, Mukherjee S, Park SJ, Skolnick J, Lee J, Im W.

Bioinformatics. 2015 Apr 8. pii: btv202. [Epub ahead of print]

PMID:
25857669
3.

Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function.

Skolnick J, Gao M, Roy A, Srinivasan B, Zhou H.

Bioorg Med Chem Lett. 2015 Mar 15;25(6):1163-70. doi: 10.1016/j.bmcl.2015.01.059. Epub 2015 Feb 3. Review.

4.

Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models.

Ando T, Skolnick J.

PLoS Comput Biol. 2014 Dec 11;10(12):e1003990. doi: 10.1371/journal.pcbi.1003990. eCollection 2014 Dec.

5.

On the role of physics and evolution in dictating protein structure and function.

Skolnick J, Gao M, Zhou H.

Isr J Chem. 2014 Aug 1;54(8-9):1176-1188.

PMID:
25484448
6.

LIGSIFT: an open-source tool for ligand structural alignment and virtual screening.

Roy A, Skolnick J.

Bioinformatics. 2015 Feb 15;31(4):539-44. doi: 10.1093/bioinformatics/btu692. Epub 2014 Oct 21.

PMID:
25336501
7.

Experimental validation of FINDSITE(comb) virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders.

Srinivasan B, Zhou H, Kubanek J, Skolnick J.

J Cheminform. 2014 Apr 26;6:16. doi: 10.1186/1758-2946-6-16. eCollection 2014.

8.

WeFold: a coopetition for protein structure prediction.

Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, Wirecki T, Cooper S, Flatten J, Xu K, Baker D, Cheng J, Delbem AC, Floudas CA, Keasar C, Levitt M, Popović Z, Scheraga HA, Skolnick J, Crivelli SN; Foldit Players.

Proteins. 2014 Sep;82(9):1850-68. doi: 10.1002/prot.24538. Epub 2014 Jul 8.

PMID:
24677212
9.

A comprehensive survey of small-molecule binding pockets in proteins.

Gao M, Skolnick J.

PLoS Comput Biol. 2013 Oct;9(10):e1003302. doi: 10.1371/journal.pcbi.1003302. Epub 2013 Oct 24.

10.
11.

Interplay of physics and evolution in the likely origin of protein biochemical function.

Skolnick J, Gao M.

Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9344-9. doi: 10.1073/pnas.1300011110. Epub 2013 May 20.

12.

Theory and simulation.

Friesner RA, Skolnick J.

Curr Opin Struct Biol. 2013 Apr;23(2):169-71. doi: 10.1016/j.sbi.2013.03.002. Epub 2013 May 18. No abstract available.

PMID:
23688932
13.

Segment assembly, structure alignment and iterative simulation in protein structure prediction.

Zhang Y, Skolnick J.

BMC Biol. 2013 Apr 15;11:44. doi: 10.1186/1741-7007-11-44. No abstract available.

14.

Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.

Jo S, Lee HS, Skolnick J, Im W.

PLoS Comput Biol. 2013;9(3):e1002946. doi: 10.1371/journal.pcbi.1002946. Epub 2013 Mar 14.

15.
16.

Are predicted protein structures of any value for binding site prediction and virtual ligand screening?

Skolnick J, Zhou H, Gao M.

Curr Opin Struct Biol. 2013 Apr;23(2):191-7. doi: 10.1016/j.sbi.2013.01.009. Epub 2013 Feb 14. Review.

17.

APoc: large-scale identification of similar protein pockets.

Gao M, Skolnick J.

Bioinformatics. 2013 Mar 1;29(5):597-604. doi: 10.1093/bioinformatics/btt024. Epub 2013 Jan 17.

18.

On the importance of hydrodynamic interactions in lipid membrane formation.

Ando T, Skolnick J.

Biophys J. 2013 Jan 8;104(1):96-105. doi: 10.1016/j.bpj.2012.11.3829. Epub 2013 Jan 8.

19.

FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach.

Zhou H, Skolnick J.

J Chem Inf Model. 2013 Jan 28;53(1):230-40. doi: 10.1021/ci300510n. Epub 2012 Dec 28.

20.

EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes.

Kumar N, Skolnick J.

Bioinformatics. 2012 Oct 15;28(20):2687-8. doi: 10.1093/bioinformatics/bts510. Epub 2012 Aug 24.

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