@article {681,
	title = {Pepitope: epitope mapping from affinity-selected peptides.},
	journal = {Bioinformatics},
	volume = {23},
	year = {2007},
	month = {2007 Dec 1},
	pages = {3244-6},
	abstract = {Identifying the epitope to which an antibody binds is central for many immunological applications such as drug design and vaccine development. The Pepitope server is a web-based tool that aims at predicting discontinuous epitopes based on a set of peptides that were affinity-selected against a monoclonal antibody of interest. The server implements three different algorithms for epitope mapping: PepSurf, Mapitope, and a combination of the two. The rationale behind these algorithms is that the set of peptides mimics the genuine epitope in terms of physicochemical properties and spatial organization. When the three-dimensional (3D) structure of the antigen is known, the information in these peptides can be used to computationally infer the corresponding epitope. A user-friendly web interface and a graphical tool that allows viewing the predicted epitopes were developed. Pepitope can also be applied for inferring other types of protein-protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure. AVAILABILITY: http://pepitope.tau.ac.il/},
	keywords = {Algorithms, Amino Acid Sequence, Binding Sites, Epitope Mapping, Molecular Sequence Data, Peptides, Protein Binding, Sequence Alignment, Sequence Analysis, Protein, Software},
	issn = {1367-4811},
	doi = {10.1093/bioinformatics/btm493},
	author = {Mayrose, Itay and Penn, Osnat and Erez, Elana and Rubinstein, Nimrod D and Shlomi, Tomer and Freund, Natalia Tarnovitski and Bublil, Erez M and Ruppin, Eytan and Sharan, Roded and Gershoni, Jonathan M and Martz, Eric and Pupko, Tal}
}
@article {684,
	title = {ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.},
	journal = {Bioinformatics},
	volume = {19},
	year = {2003},
	month = {2003 Jan},
	pages = {163-4},
	abstract = {We recently developed algorithmic tools for the identification of functionally important regions in proteins of known three dimensional structure by estimating the degree of conservation of the amino-acid sites among their close sequence homologues. Projecting the conservation grades onto the molecular surface of these proteins reveals patches of highly conserved (or occasionally highly variable) residues that are often of important biological function. We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins. AVAILABILITY: The ConSurf web server is available at:http://consurf.tau.ac.il. SUPPLEMENTARY INFORMATION: A set of examples is available at http://consurf.tau.ac.il under {\textquoteright}GALLERY{\textquoteright}.},
	keywords = {Amino Acids, bcl-X Protein, Conserved Sequence, Databases, Protein, Evolution, Molecular, Internet, Phylogeny, Protein Conformation, Proteins, Proto-Oncogene Proteins c-bcl-2, Sequence Alignment, Sequence Analysis, Protein, User-Computer Interface},
	issn = {1367-4803},
	author = {Glaser, Fabian and Pupko, Tal and Paz, Inbal and Bell, Rachel E and Bechor-Shental, Dalit and Martz, Eric and Ben-Tal, Nir}
}
@article {685,
	title = {Protein Explorer: easy yet powerful macromolecular visualization.},
	journal = {Trends Biochem Sci},
	volume = {27},
	year = {2002},
	month = {2002 Feb},
	pages = {107-9},
	abstract = {Protein Explorer (PE, http://www.proteinexplorer.org) enables students, educators and other nonspecialists to visualize macromolecular structures easily. It also offers several advanced capabilities useful to protein structure specialists. Great attention has been given to making PE easy to use. Explanations, color keys and troubleshooting information are displayed automatically. There are also {\textquoteright}Frequently Asked Questions{\textquoteright}, a one-hour {\textquoteright}Quick-Tour{\textquoteright}, an alphabetical {\textquoteright}Help/Index/Glossary{\textquoteright}, and a detailed {\textquoteright}Tutorial{\textquoteright}; all making PE much easier to use than either Chime or RasMol. Moreover, it is much more powerful; in addition to basic macromolecular visualization capabilities common to most similar programs, it offers one-click visualization of interfaces between moieties ({\textquoteright}contacts{\textquoteright}), cation-pi interactions and salt bridges, as well as easy-to-use routines to visualize regions of conservation in three-dimensional protein structures based on multiple sequence alignments.},
	keywords = {Computational Biology, DNA, Evolution, Molecular, Macromolecular Substances, Protein Structure, Secondary, Proteins, Sequence Alignment, Software},
	issn = {0968-0004},
	author = {Martz, Eric}
}
