Snoeyink J - Search Results

1

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.

O'Meara MJ, Leaver-Fay A, Tyka MD, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B. O'Meara MJ, et al. Among authors: snoeyink j. J Chem Theory Comput. 2015 Feb 10;11(2):609-22. doi: 10.1021/ct500864r. J Chem Theory Comput. 2015. PMID: 25866491 Free PMC article.

2

Scientific benchmarks for guiding macromolecular energy function improvement.

Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, Baker D, Kuhlman B. Leaver-Fay A, et al. Among authors: snoeyink j. Methods Enzymol. 2013;523:109-43. doi: 10.1016/B978-0-12-394292-0.00006-0. Methods Enzymol. 2013. PMID: 23422428 Free PMC article.

3

An adaptive dynamic programming algorithm for the side chain placement problem.

Leaver-Fay A, Kuhlman B, Snoeyink J. Leaver-Fay A, et al. Among authors: snoeyink j. Pac Symp Biocomput. 2005:16-27. Pac Symp Biocomput. 2005. PMID: 15759610 Free article.

4

Maintaining solvent accessible surface area under rotamer substitution for protein design.

Leaver-Fay A, Butterfoss GL, Snoeyink J, Kuhlman B. Leaver-Fay A, et al. Among authors: snoeyink j. J Comput Chem. 2007 Jun;28(8):1336-41. doi: 10.1002/jcc.20626. J Comput Chem. 2007. PMID: 17285560

5

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB 3rd, Snoeyink J, Richardson JS, Richardson DC. Davis IW, et al. Among authors: snoeyink j. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83. doi: 10.1093/nar/gkm216. Epub 2007 Apr 22. Nucleic Acids Res. 2007. PMID: 17452350 Free PMC article.

6

Structure-based function inference using protein family-specific fingerprints.

Bandyopadhyay D, Huan J, Liu J, Prins J, Snoeyink J, Wang W, Tropsha A. Bandyopadhyay D, et al. Among authors: snoeyink j. Protein Sci. 2006 Jun;15(6):1537-43. doi: 10.1110/ps.062189906. Protein Sci. 2006. PMID: 16731985 Free PMC article.

7

Distance-based identification of structure motifs in proteins using constrained frequent subgraph mining.

Huan J, Bandyopadhyay D, Prins J, Snoeyink J, Tropsha A, Wang W. Huan J, et al. Among authors: snoeyink j. Comput Syst Bioinformatics Conf. 2006:227-38. Comput Syst Bioinformatics Conf. 2006. PMID: 17369641 Free article.

8

Multiple structure alignment by optimal RMSD implies that the average structure is a consensus.

Wang X, Snoeyink J. Wang X, et al. Among authors: snoeyink j. Comput Syst Bioinformatics Conf. 2006:79-87. Comput Syst Bioinformatics Conf. 2006. PMID: 17369627 Free article.

9

Comparing graph representations of protein structure for mining family-specific residue-based packing motifs.

Huan J, Bandyopadhyay D, Wang W, Snoeyink J, Prins J, Tropsha A. Huan J, et al. Among authors: snoeyink j. J Comput Biol. 2005 Jul-Aug;12(6):657-71. doi: 10.1089/cmb.2005.12.657. J Comput Biol. 2005. PMID: 16108709

10

RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.

Wang X, Kapral G, Murray L, Richardson D, Richardson J, Snoeyink J. Wang X, et al. Among authors: snoeyink j. J Math Biol. 2008 Jan;56(1-2):253-78. doi: 10.1007/s00285-007-0082-x. Epub 2007 Mar 31. J Math Biol. 2008. PMID: 17401565 Free PMC article.

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