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1
SURFACE: a database of protein surface regions for functional annotation.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D240-4. doi: 10.1093/nar/gkh054.
2
Functional annotation by identification of local surface similarities: a novel tool for structural genomics.
BMC Bioinformatics. 2005 Aug 2;6:194. doi: 10.1186/1471-2105-6-194.
3
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D217-22. doi: 10.1093/nar/gkh095.
4
The LabelHash server and tools for substructure-based functional annotation.
Bioinformatics. 2011 Aug 1;27(15):2161-2. doi: 10.1093/bioinformatics/btr343. Epub 2011 Jun 8.
5
A library of protein surface patches discriminates between native structures and decoys generated by structure prediction servers.
BMC Struct Biol. 2011 May 4;11(1):20. doi: 10.1186/1472-6807-11-20.
6
Clustering the annotation space of proteins.
BMC Bioinformatics. 2005 Feb 9;6:24. doi: 10.1186/1471-2105-6-24.
7
SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.
Nucleic Acids Res. 2010 Jan;38(Database issue):D223-6. doi: 10.1093/nar/gkp949. Epub 2009 Nov 11.
8
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D245-50. doi: 10.1093/nar/gkh064.
9
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites.
Nucleic Acids Res. 2007 Jan;35(Database issue):D229-31. doi: 10.1093/nar/gkl922. Epub 2006 Nov 16.
10
Superpose3D: a local structural comparison program that allows for user-defined structure representations.
PLoS One. 2010 Aug 5;5(8):e11988. doi: 10.1371/journal.pone.0011988.

引用本文的文献

1
Diffusion accessibility as a method for visualizing macromolecular surface geometry.
Protein Sci. 2015 Oct;24(10):1702-5. doi: 10.1002/pro.2752. Epub 2015 Aug 6.
2
Computational methods in drug discovery.
Pharmacol Rev. 2013 Dec 31;66(1):334-95. doi: 10.1124/pr.112.007336. Print 2014.
3
Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.
Proteins. 2012 Apr;80(4):1177-95. doi: 10.1002/prot.24018. Epub 2012 Jan 24.
4
Structure- and sequence-based function prediction for non-homologous proteins.
J Struct Funct Genomics. 2012 Jun;13(2):111-23. doi: 10.1007/s10969-012-9126-6. Epub 2012 Jan 22.
5
Protein surface characterization using an invariant descriptor.
Int J Biomed Imaging. 2011;2011:918978. doi: 10.1155/2011/918978. Epub 2011 Nov 22.
6
Binding ligand prediction for proteins using partial matching of local surface patches.
Int J Mol Sci. 2010;11(12):5009-26. doi: 10.3390/ijms11125009. Epub 2010 Dec 6.
7
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1(Suppl 1):S35. doi: 10.1186/1471-2105-12-S1-S35.
8
3V: cavity, channel and cleft volume calculator and extractor.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W555-62. doi: 10.1093/nar/gkq395. Epub 2010 May 16.
9
Real-time ligand binding pocket database search using local surface descriptors.
Proteins. 2010 Jul;78(9):2007-28. doi: 10.1002/prot.22715.
10
A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity.
PLoS One. 2009 Jul 15;4(7):e6266. doi: 10.1371/journal.pone.0006266.

本文引用的文献

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Prediction of protein function from protein sequence and structure.
Q Rev Biophys. 2003 Aug;36(3):307-40. doi: 10.1017/s0033583503003901.
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Identification of protein functions from a molecular surface database, eF-site.
J Struct Funct Genomics. 2002;2(1):9-22. doi: 10.1023/a:1011318527094.
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ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
Nucleic Acids Res. 2003 Jul 1;31(13):3625-30. doi: 10.1093/nar/gkg545.
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The Protein Data Bank and structural genomics.
Nucleic Acids Res. 2003 Jan 1;31(1):489-91. doi: 10.1093/nar/gkg068.
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The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Nucleic Acids Res. 2003 Jan 1;31(1):365-70. doi: 10.1093/nar/gkg095.
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A new method to detect related function among proteins independent of sequence and fold homology.
J Mol Biol. 2002 Oct 18;323(2):387-406. doi: 10.1016/s0022-2836(02)00811-2.
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Structural proteomics: the potential of high-throughput structure determination.
Trends Microbiol. 2002;10(10 Suppl):S27-31. doi: 10.1016/s0966-842x(02)02443-5.
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MINT: a Molecular INTeraction database.
FEBS Lett. 2002 Feb 20;513(1):135-40. doi: 10.1016/s0014-5793(01)03293-8.
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The PROSITE database, its status in 2002.
Nucleic Acids Res. 2002 Jan 1;30(1):235-8. doi: 10.1093/nar/30.1.235.
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Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution.
J Mol Biol. 2000 Nov 3;303(4):455-65. doi: 10.1006/jmbi.2000.4151.

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