Parmodel: a web server for automated comparative modeling of proteins

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Author(s):	Uchôa, Hugo Brandão ; Jorge, Guilherme Eberhart ; Silveira, Nelson José Freitas da ; Camera Júnior, João Carlos ; Canduri, Fernanda ; Azevedo Júnior, Walter Filgueira de ^[6] Total Authors: 6
Document type:	Journal article
Source:	Biochemical and Biophysical Research Communications; v. 325, n. 4, p. 1481-1486, Dec. 2004.
Abstract
Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models for a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools/parmodel. (AU)

FAPESP's process:	01/07532-0 - Structural genomics of cyclin dependent kinases and plant defensive proteinases and their natural inhibitors
Grantee:	Walter Filgueira de Azevedo Junior
Support Opportunities:	Regular Research Grants