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PUDGE: a flexible, interactive server for protein structure prediction.

ABSTRACT: The construction of a homology model for a protein can involve a number of decisions requiring the integration of different sources of information and the application of different modeling tools depending on the particular problem. Functional information can be especially important in guiding the modeling process, but such information is not generally integrated into modeling pipelines. Pudge is a flexible, interactive protein structure prediction server, which is designed with these issues in mind. By dividing the modeling into five stages (template selection, alignment, model building, model refinement and model evaluation) and providing various tools to visualize, analyze and compare the results at each stage, we enable a flexible modeling strategy that can be tailored to the needs of a given problem. Pudge is freely available at http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PUDGE.

SUBMITTER: Norel R

PROVIDER: S-EPMC2896183 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

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PUDGE: a flexible, interactive server for protein structure prediction.

Norel Raquel R Petrey Donald D Honig Barry B

Nucleic acids research 20100604 Web Server issue

The construction of a homology model for a protein can involve a number of decisions requiring the integration of different sources of information and the application of different modeling tools depending on the particular problem. Functional information can be especially important in guiding the modeling process, but such information is not generally integrated into modeling pipelines. Pudge is a flexible, interactive protein structure prediction server, which is designed with these issues in m ...[more]

PMID: 20525783

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