ModView logo
ModView new page


Developed by
Valentin Ilyin
Please send any ModView
comments and suggestions
Some ModView Highlights

ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. As a Netscape plugin,like Chime , it can be embed into Web pages and controlled by Javascript objects on the page. It has wide range of tools to manipulate and analyze sequences and structures by interactive control

... ModView as Front-end interface to biodatabases

Modview can easily interface with local or remote bioresources to provide GUI and analytical tools. Currently ModView is used as a database interface in several structure-sequence protein resources.
  • ModBase, a Database of Comparative Protein Structure Models, (Pieper et. al, Nuc.Acid.Res.)
  • LigBase, a Structural Database of Aligned Ligand Binding Protein Sequences, (Stuart et al., Bioinformatics).
  • DBAli, a Database of Sequence-Structure alignments, (Marti-Renom et. al.2001,Bioinformatics).
  • ModView can be also used to view structures and sequences in Protein Data Bank , choose 'Rasmol' display option on View Structure window.
  • ... ModView provides Protein Family analysis.

    Two families of DNA binding proteins have been analysed by ModView. The scalable multiple alignment with combination of visualization of structural features of molecules cleary shows invariant residues involved in DNA binding in Zinc finger protein superfamily (ZFP) and superfamily of the DNA-Binding Domain Of The Replication Initiation Protein E1 From Papillomavirus (RIP). These two families also shows different pictures of homology tree. ZFP family has ~50% identity among all the members, while RIP family can be subdivided in several closely related subfamilies. (Ilyin and Sali, 2001, CSHL).

    Recently, ModView facilitates the target selection process for New York Structural Genomics Research Consortium, by providing integrative visual analyses of the comparative protein models, PSI-BLAST profile and phylogenetic data of protein targets selected for novel structures determination (Bonanno et. al. 2001, PNAS).

    ... ModView References.

    * V.A.Ilyin, U. Pieper, A. C. Stuart, M. A. Mart-Renom and A. Sali. Analysis and Visualization of Multiple Biomolecule Structures and Sequences by ModView. (submitted)

    * Ursula Pieper, Narayanan Eswar, Ashley C. Stuart, Valentin A. Ilyin and Andrej Sali, MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research. 2002. Jan 1: 30(1):255-9. PubMed

    * Stuart A.C., Ilyin V.A., and Sali A., (2001) LigBase: A Database of Families of Aligned Ligand Binding Sites in Known Protein Sequences and Structures, Bioinformatics 2002 Jan;18(1):200-1 PubMed

    * Jeffrey B. Bonanno, Carme Edo, Narayanan Eswar, Urusla Pieper, Valentin Ilyin, Michael J. Romanowski, Sue Ellen Gerhaman, Helen Kycia, F. William Sudier, Andrej Sali, Stephen Burley. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proc Natl Acad Sci U S A 2001 Nov 6;98(23):12896-901. PubMed

    * Valentin Ilyin and Andrej Sali. Protein superfamily analysis by ModView. CSHL meeting. Aug.8, 2001.

    * Marti-Renom, M.A., Ilyin V.A., Sali, A. DBAli: A database of protein structure alignments. Bioinformatics. p.746. Vol. 17 no 8, 2001. PubMed

    Modview uses Roger Sayle's Rasmol rendering system and modified alignment editor panel from Michele Clamp's Jalview.

    Rockefeller University Logo ModView is developed and maintained by Valentin ILYIN in the laboratory of Andrej Sali ,Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Ave, New York, NY 10021. ModView is copyright © 2001. Any selling of the original, modified or parts of the program is prohibited without a written permission from the authors.

    last updated on Mar 8, 2001.