@article {676,
	title = {Proteopedia: a status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules.},
	journal = {J Struct Biol},
	volume = {175},
	year = {2011},
	month = {2011 Aug},
	pages = {244-52},
	abstract = {Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other biomolecule structures. Created as a means for communicating biomolecule structures to a diverse scientific audience, Proteopedia (http://www.proteopedia.org) presents structural annotation in an intuitive, interactive format and allows members of the scientific community to easily contribute their own annotations. Here, we provide a status report on Proteopedia by describing advances in the web resource since its inception three and a half years ago, focusing on features of potential direct use to the scientific community. We discuss its progress as a collaborative 3D-encyclopedia of structures as well as its use as a complement to scientific publications and PowerPoint presentations. We also describe Proteopedia{\textquoteright}s use for 3D visualization in structure-related pedagogy.},
	keywords = {Encyclopedias as Topic, Information Dissemination, Information Management, Information Services, Models, Molecular, Molecular Biology, Online Systems, Protein Conformation, Proteins, User-Computer Interface},
	issn = {1095-8657},
	doi = {10.1016/j.jsb.2011.04.011},
	author = {Prilusky, Jaime and Hodis, Eran and Canner, David and Decatur, Wayne A and Oberholser, Karl and Martz, Eric and Berchanski, Alexander and Harel, Michal and Sussman, Joel L}
}
@article {679,
	title = {Proteopedia.Org: a scientific "Wiki" bridging the rift between 3D structure and function of biomacromolecules.},
	journal = {Biopolymers},
	volume = {92},
	year = {2009},
	month = {2009},
	pages = {76-7},
	keywords = {Computational Biology, Imaging, Three-Dimensional, Internet, Models, Molecular, Protein Structure, Quaternary, Protein Structure, Tertiary, Proteins, Structure-Activity Relationship},
	issn = {0006-3525},
	doi = {10.1002/bip.21126},
	author = {Martz, Eric}
}
@article {680,
	title = {Proteopedia - a scientific {\textquoteright}wiki{\textquoteright} bridging the rift between three-dimensional structure and function of biomacromolecules.},
	journal = {Genome Biol},
	volume = {9},
	year = {2008},
	month = {2008},
	pages = {R121},
	abstract = {Many scientists lack the background to fully utilize the wealth of solved three-dimensional biomacromolecule structures. Thus, a resource is needed to present structure/function information in a user-friendly manner to a broad scientific audience. Proteopedia http://www.proteopedia.org is an interactive, wiki web-resource whose pages have embedded three-dimensional structures surrounded by descriptive text containing hyperlinks that change the appearance (view, representations, colors, labels) of the adjacent three-dimensional structure to reflect the concept explained in the text.},
	keywords = {Databases, Protein, Internet, Models, Molecular, Protein Conformation, Protein Structure, Tertiary, Proteins, Software},
	issn = {1465-6914},
	doi = {10.1186/gb-2008-9-8-r121},
	author = {Hodis, Eran and Prilusky, Jaime and Martz, Eric and Silman, Israel and Moult, John and Sussman, Joel L}
}
@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 {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}
}
