Automated function prediction in protein structures
Citations and publications

If you use the SeqFEATURE models or data from the PDB scan in your research, please cite the following paper:

Wu S, Liang MP, Altman RB. The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. Genome Biology 2008, 9:R8 PMID: 18197987

If you use any of the other models or the interactive results pages in your research, please also cite this paper:

Liang MP, Banatao DR, Klein TE, Brutlag DL, Altman RB. "WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures." Nucleic Acids Res. 2003 Jul 1;31(13):3324-7. [PMID: 12824318]

Other publications:

Buturović L, Wong M, Tang GW, Altman RB, Petković D (2014)
High Precision Prediction of Functional Sites in Protein Structures.
PLoS ONE 2014 Feb 11; PONE-D-13-39539R1, EMID: b17311ed7a971c30

Lahti J., Tang G., Capriotti E., Liu T.
Bioinformatics and variability in drug response: a protein structural perspective.
J R Soc Interface. 2012 Jul 7;9(72):1409-37 doi: 10.1098/rsif.2011.0843 PMID: 22552919

Liu T., Altman RB.
Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding.
PLoS Comput Biol. 2011 Dec 29;7(12): e1002326. doi:10.1371/journal.pcbi 1002326. PMID: 22219723

Tang G., Altman RB.
Remote Thioredoxin Recognition Using Evolutionary Conservation and Structural Dynamics.
Structure 2011 Apr 13;19(4):461-470. PMID: 21481770

Wu S., Liu T., Altman RB.
Identification of Recurring Protein Structure Microenvironments and Discover of Novel Functional Sites around CYS Residues.
BMC Structural Biology. 2010 Feb 2;10(4) doi:10.1186/1472-6807-10-4 PMID: 20122268

Yoon S, Ebert JC, Chung EY, Di Micheli G, Altman RB.
Clustering protein environments for function predictions: finding PROSITE motifs in 3D.
BMC Bioinform. 2007 May 22;8(Suppl 4):S10. PMID: 17570144

Banatao DR, Altman RB, Klein TE.
Microenvironment analysis and identification of magnesium binding sites in RNA.
Nucleic Acids Res. 2003 Aug 1;31(15):4450-60. PMID: 12888505

Liang MP, Banatao DR, Klein TE, Brutlag DL, Altman RB.
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular struc tures.
Nucleic Acids Res. 2003 Jul 1;31(13):3324-7. PMID: 12824318

Wei L, Altman RB. Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function.
J Bioinform Comput Biol. 2003 Apr;1(1):119-38. PMID: 15290784

Liang MP, Brutlag DL, Altman RB.
Automated construction of structural motifs for predicting functional sites on protein structures.
Pac Symp Biocomput. 2003;:204-15. PMID: 12603029

Waugh A, Williams GA, Wei L, Altman RB.
Using meta computing tools to facilitate large-scale analyses of biological databases.
Pac Symp Biocomput. 2001;:360-71. PMID: 11262955

Banatao DR, Huang CC, Babbitt PC, Altman RB, Klein TE.
ViewFeature: integrated feature analysis and visualization.
Pac Symp Biocomput. 2001;:240-50. PMID: 11262944

Wei L, Huang ES, Altman RB.
Are predicted structures good enough to preserve functional sites?
Structure Fold Des. 1999 Jun 15;7(6):643-50. PMID: 10404593

Wei L, Altman RB.
Recognizing protein binding sites using statistical descriptions of their 3D environments.
Pac Symp Biocomput. 1998;:497-508. PMID: 9697207

Wei L, Altman RB, Chang JT.
Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences.
Pac Symp Biocomput. 1997;:465-76. PMID: 9390315

Bagley SC, Altman RB.
Conserved features in the active site of nonhomologous serine proteases.
Fold Des. 1996;1(5):371-9. PMID: 9080183

Bagley SC, Altman RB.
Characterizing the microenvironment surrounding protein sites.
Protein Sci. 1995 Apr;4(4):622-35. PMID: 7613462

Bagley SC, Wei L, Cheng C, Altman RB.
Characterizing oriented protein structural sites using biochemical properties.
Proc Int Conf Intell Syst Mol Biol. 1995;3:12-20. PMID: 7584427

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