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Results: 1 to 20 of 231

1.

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.

PMID:
24936211
[PubMed]
Free PMC Article
2.

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, Players F.

Proteins. 2014 Feb 15. doi: 10.1002/prot.24538. [Epub ahead of print]

PMID:
24677212
[PubMed - as supplied by publisher]
3.

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.

PMID:
24204237
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: algorithm and limitations.

Ando T, Chow E, Skolnick J.

J Chem Phys. 2013 Sep 28;139(12):121922. doi: 10.1063/1.4817660.

PMID:
24089734
[PubMed - indexed for MEDLINE]
5.

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.

PMID:
23690621
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
23587325
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
23516343
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23415854
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
23335017
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
23332062
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
23240691
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
22923291
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Krylov subspace methods for computing hydrodynamic interactions in brownian dynamics simulations.

Ando T, Chow E, Saad Y, Skolnick J.

J Chem Phys. 2012 Aug 14;137(6):064106. doi: 10.1063/1.4742347.

PMID:
22897254
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Career accomplishments of Harold A. Scheraga.

Hammes GG, Skolnick J.

J Phys Chem B. 2012 Jun 14;116(23):6569-71. doi: 10.1021/jp211866v. No abstract available.

PMID:
22697899
[PubMed - indexed for MEDLINE]
16.

FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs.

Zhou H, Skolnick J.

Mol Pharm. 2012 Jun 4;9(6):1775-84. doi: 10.1021/mp3000716. Epub 2012 May 21.

PMID:
22574683
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation.

Gao M, Skolnick J.

Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3784-9. doi: 10.1073/pnas.1117768109. Epub 2012 Feb 21.

PMID:
22355140
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Further evidence for the likely completeness of the library of solved single domain protein structures.

Skolnick J, Zhou H, Brylinski M.

J Phys Chem B. 2012 Jun 14;116(23):6654-64. doi: 10.1021/jp211052j. Epub 2012 Feb 13.

PMID:
22272723
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Template-based protein structure modeling using TASSER(VMT).

Zhou H, Skolnick J.

Proteins. 2011 Sep 14. doi: 10.1002/prot.23183. [Epub ahead of print]

PMID:
22105797
[PubMed - as supplied by publisher]
Free PMC Article
20.

GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction.

Zhou H, Skolnick J.

Biophys J. 2011 Oct 19;101(8):2043-52. doi: 10.1016/j.bpj.2011.09.012.

PMID:
22004759
[PubMed - indexed for MEDLINE]
Free PMC Article

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