title: PI2PE: protein interface/interior prediction engine.
abstract: The side chains of the 20 types of amino acids, owing to a large extent to their different physical properties, have characteristic distributions in interior/surface regions of individual proteins and in interface/non-interface portions of protein surfaces that bind proteins or nucleic acids. These distributions have important structural and functional implications. We have developed accurate methods for predicting the solvent accessibility of amino acids from a protein sequence and for predicting interface residues from the structure of a protein-binding or DNA-binding protein. The methods are called WESA, cons-PPISP and DISPLAR, respectively. The web servers of these methods are now available at http://pipe.scs.fsu.edu. To illustrate the utility of these web servers, cons-PPISP and DISPLAR predictions are used to construct a structural model for a multicomponent protein-DNA complex.
authors.affiliation: Institute of Molecular Biophysics and School of Computational Science and Department of Physics, Florida State University, Tallahassee, FL 32306, USA.
authors.forename: Harianto
authors.initials: H
authors.lastname: Tjong
authors.forename: Sanbo
authors.initials: S
authors.lastname: Qin
authors.forename: Huan-Xiang
authors.initials: HX
authors.lastname: Zhou
mesh_terms: D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D020407:Internet; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D008565:Membrane Proteins; D011506:Proteins; D004247:DNA