PUDGE: a flexible, interactive server for protein structure prediction.
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.
Norel
Raquel
R
Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA. rn98@columbia.edu
Petrey
Donald
D
Honig
Barry
B
D001426:Bacterial Proteins / Q000737:chemistry; D020407:Internet; D008958:Models, Molecular; D012984:Software; D040681:Structural Homology, Protein; D014584:User-Computer Interface
D001426:Bacterial Proteins