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. "A comprehensive scan of the Protein Data Bank with the SeqFEATURE library of functional site models and prediction of function for structural genomics targets." Genome Biology (in review)

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]

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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