Methods for Protein Structure Prediction - Fox Chase Cancer Center

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Available databases, software, and services • Rotamer library • ProtBuD -- biological units database across families • PISCES -- non-redundant sequences in PDB • SCWRL3 • MolIDE 1.5 • ArboDraw -- drawing phylogenetic trees • BioDownloader -- automatic updating of biological databases http://dunbrack.fccc.edu
Fox Chase Cancer Center Molecular Modeling Facility • Since April 2003, funded by NCI Cancer Center Support Grant and Pew Charitable Trusts • One staff member (Mark Andrake, Ph.D.) • Services: – Protein database search, multiple sequence alignments, orthologues/paralogues, phylogenetic trees – Homology modeling based on PDB templates – Secondary structure, coiled-coil, transmembrane topology prediction – Conservation analysis with structural interpretation – Interpretation and design of mutations – Docking of small molecules, proteins, nucleic acids – Text and images for papers and grants – Installation and instruction in structure visualization – Custom software for specific projects http://dunbrack.fccc.edu
Page 1 and 2: Methods for Protein Structure Predi
Page 3 and 4: Targets involved in DNA repair, apo
Page 5 and 6: CBS Domains of Cystathionine Beta S
Page 7 and 8: Q556H W557S W557G W557R V559A V559C
Page 9 and 10: Designing new mutations to affect f
Page 11 and 12: Hints at function Human SULT4A1 Sul
Page 13 and 14: Identification and Alignment Search
Page 15 and 16: Loop modeling Shift in loop Deletio
Page 17 and 18: Always requires: Prediction at Each
Page 19 and 20: Backbone-dependent rotamer library
Page 21 and 22: 2900 licenses in 73 countries SCWRL
Page 23: Future technologies • Modeling of

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