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Results: 1 to 20 of 33

1.

DINC: a new AutoDock-based protocol for docking large ligands.

Dhanik A, McMurray JS, Kavraki LE.

BMC Struct Biol. 2013;13 Suppl 1:S11. doi: 10.1186/1472-6807-13-S1-S11. Epub 2013 Nov 8.

PMID:
24564952
[PubMed - in process]
Free PMC Article
2.

SIMS: a hybrid method for rapid conformational analysis.

Gipson B, Moll M, Kavraki LE.

PLoS One. 2013 Jul 23;8(7):e68826. doi: 10.1371/journal.pone.0068826. Print 2013.

PMID:
23935893
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome.

Bryant DH, Moll M, Finn PW, Kavraki LE.

PLoS Comput Biol. 2013;9(6):e1003087. doi: 10.1371/journal.pcbi.1003087. Epub 2013 Jun 6.

PMID:
23754939
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Binding modes of peptidomimetics designed to inhibit STAT3.

Dhanik A, McMurray JS, Kavraki LE.

PLoS One. 2012;7(12):e51603. doi: 10.1371/journal.pone.0051603. Epub 2012 Dec 12.

PMID:
23251591
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Computational models of protein kinematics and dynamics: beyond simulation.

Gipson B, Hsu D, Kavraki LE, Latombe JC.

Annu Rev Anal Chem (Palo Alto Calif). 2012;5:273-91. doi: 10.1146/annurev-anchem-062011-143024. Epub 2012 Apr 9. Review.

PMID:
22524225
[PubMed - indexed for MEDLINE]
6.

An algorithm for efficient identification of branched metabolic pathways.

Heath AP, Bennett GN, Kavraki LE.

J Comput Biol. 2011 Nov;18(11):1575-97. doi: 10.1089/cmb.2011.0165. Epub 2011 Oct 14.

PMID:
21999288
[PubMed - indexed for MEDLINE]
7.

The LabelHash server and tools for substructure-based functional annotation.

Moll M, Bryant DH, Kavraki LE.

Bioinformatics. 2011 Aug 1;27(15):2161-2. doi: 10.1093/bioinformatics/btr343. Epub 2011 Jun 8.

PMID:
21659320
[PubMed - indexed for MEDLINE]
Free Article
8.

The LabelHash algorithm for substructure matching.

Moll M, Bryant DH, Kavraki LE.

BMC Bioinformatics. 2010 Nov 11;11:555. doi: 10.1186/1471-2105-11-555.

PMID:
21070651
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Tracing conformational changes in proteins.

Haspel N, Moll M, Baker ML, Chiu W, Kavraki LE.

BMC Struct Biol. 2010 May 17;10 Suppl 1:S1. doi: 10.1186/1472-6807-10-S1-S1.

PMID:
20487508
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction.

Bryant DH, Moll M, Chen BY, Fofanov VY, Kavraki LE.

BMC Bioinformatics. 2010 May 11;11:242. doi: 10.1186/1471-2105-11-242.

PMID:
20459833
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Finding metabolic pathways using atom tracking.

Heath AP, Bennett GN, Kavraki LE.

Bioinformatics. 2010 Jun 15;26(12):1548-55. doi: 10.1093/bioinformatics/btq223. Epub 2010 Apr 25.

PMID:
20421197
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides.

Stamati H, Clementi C, Kavraki LE.

Proteins. 2010 Feb 1;78(2):223-35. doi: 10.1002/prot.22526.

PMID:
19731366
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Multiscale characterization of protein conformational ensembles.

Shehu A, Kavraki LE, Clementi C.

Proteins. 2009 Sep;76(4):837-51. doi: 10.1002/prot.22390.

PMID:
19280604
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb-C and its complement target C3d.

Haspel N, Ricklin D, Geisbrecht BV, Kavraki LE, Lambris JD.

Protein Sci. 2008 Nov;17(11):1894-906. doi: 10.1110/ps.036624.108. Epub 2008 Aug 7.

PMID:
18687868
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Unfolding the fold of cyclic cysteine-rich peptides.

Shehu A, Kavraki LE, Clementi C.

Protein Sci. 2008 Mar;17(3):482-93. doi: 10.1110/ps.073142708.

PMID:
18287281
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O.

BMC Bioinformatics. 2008 Jan 11;9:17. doi: 10.1186/1471-2105-9-17.

PMID:
18190718
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction.

Moll M, Kavraki LE.

Comput Syst Bioinformatics Conf. 2008;7:157-68.

PMID:
19642277
[PubMed - indexed for MEDLINE]
Free Article
18.

Roadmap methods for protein folding.

Moll M, Schwarz D, Kavraki LE.

Methods Mol Biol. 2008;413:219-39. Review.

PMID:
18075168
[PubMed - indexed for MEDLINE]
19.

Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

Chen BY, Bryant DH, Cruess AE, Bylund JH, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE.

Comput Syst Bioinformatics Conf. 2007;6:343-55.

PMID:
17951837
[PubMed - indexed for MEDLINE]
Free Article
20.

The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.

Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE.

J Comput Biol. 2007 Jul-Aug;14(6):791-816.

PMID:
17691895
[PubMed - indexed for MEDLINE]

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