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Items: 1 to 20 of 73

1.

Travel depth, a new shape descriptor for macromolecules: application to ligand binding.

Coleman RG, Sharp KA.

J Mol Biol. 2006 Sep 22;362(3):441-58. Epub 2006 Jul 15.

PMID:
16934837
2.

Fast surface-based travel depth estimation algorithm for macromolecule surface shape description.

Giard J, Alface PR, Gala JL, Macq B.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):59-68. doi: 10.1109/TCBB.2009.53.

PMID:
21071797
3.

Protein pockets: inventory, shape, and comparison.

Coleman RG, Sharp KA.

J Chem Inf Model. 2010 Apr 26;50(4):589-603. doi: 10.1021/ci900397t.

4.

Macromolecular recognition.

Deremble C, Lavery R.

Curr Opin Struct Biol. 2005 Apr;15(2):171-5. Review.

PMID:
15837175
5.
6.

Comprehensive identification of "druggable" protein ligand binding sites.

An J, Totrov M, Abagyan R.

Genome Inform. 2004;15(2):31-41.

PMID:
15706489
7.

Measuring the differential stoichiometry and energetics of ligand binding to macromolecules by single-molecule force spectroscopy: an extended theory.

Jacobson DR, Saleh OA.

J Phys Chem B. 2015 Feb 5;119(5):1930-8. doi: 10.1021/jp511555g. Epub 2015 Jan 26.

PMID:
25621932
8.
9.

RNAmap2D - calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures.

Pietal MJ, Szostak N, Rother KM, Bujnicki JM.

BMC Bioinformatics. 2012 Dec 21;13:333. doi: 10.1186/1471-2105-13-333.

10.

Investigation of atomic level patterns in protein--small ligand interactions.

Chen K, Kurgan L.

PLoS One. 2009;4(2):e4473. doi: 10.1371/journal.pone.0004473. Epub 2009 Feb 16.

11.

A method for localizing ligand binding pockets in protein structures.

Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM.

Proteins. 2006 Feb 1;62(2):479-88.

PMID:
16304646
13.

Surface solid angle-based site points for molecular docking.

Hendrix DK, Kuntz ID.

Pac Symp Biocomput. 1998:317-26.

14.

Pocketome via comprehensive identification and classification of ligand binding envelopes.

An J, Totrov M, Abagyan R.

Mol Cell Proteomics. 2005 Jun;4(6):752-61. Epub 2005 Mar 9.

15.

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.

16.

Three-dimensional computation of atom depth in complex molecular structures.

Varrazzo D, Bernini A, Spiga O, Ciutti A, Chiellini S, Venditti V, Bracci L, Niccolai N.

Bioinformatics. 2005 Jun 15;21(12):2856-60. Epub 2005 Apr 12.

PMID:
15827080
17.

Extraction, quantification and visualization of protein pockets.

Zhang X, Bajaj C.

Comput Syst Bioinformatics Conf. 2007;6:275-86.

18.

Adepth: New Representation and its implications for atomic depths of macromolecules.

Chen SW, Pellequer JL.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W412-6. doi: 10.1093/nar/gkt299. Epub 2013 Apr 22.

19.

Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape.

Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S.

Proteins. 1998 Oct 1;33(1):1-17.

PMID:
9741840
20.

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