Second Biennial
UCSC-QB3 Symposium on Bioinformatics:
Predicting the structure and function of proteins

(Informal post-CASP Workshop)
Earth & Marine B206
University of California, Santa Cruz
7-8 Dec 2002

This is a tentative schedule of speakers for the symposium. Talks may have to be moved to accomodate constraints of speakers, and open slots may be filled by speakers who sign up later.

Saturday 7 Dec 2002

TimeSpeakerTitle
9:00Kevin KarplusUnifying secondary-structure, fold-recognition, and new-fold methods for protein structure prediction
9:30Arne ElofssonA study of automated measures for benchmarks of fold recognition methods
10:00Bjørn WallnerCan correct protein models be identified?
10:30Coffee
11:00Carol RohlLoop Modeling using Rosetta
11:30Charlie StraussMAMMOTH structure-structure comparison
12:00Lunch
1:30Gabriel del RioAssessing the structure/function relationship of biological networks:
From DNA microarray data analysis to protein structure prediction
2:00Robert BaertschImproving gene prediction with pseudogenes
A novel use for mouse-human synteny to finish the genome
2:30Coffee
3:00Matt JacobsonPLOP (Protein Local Optimization Program): A New Software Platform for Predictive Protein Modeling Using All-Atom Force Fields and Implicit Solvation
3:30Andrei LomizeNew energy functions for protein modeling derived from thermodynamic data
4:00Kimmen SjölanderPhylogenetic trees, Subfamily HMMs, Modeller expertise, and sleep deprivation for 4 months straight: The UC Berkeley approach to CASP5

Sunday 8 Dec 2002

TimeSpeakerTitle
9:00Chris Bystroff Contact map threading using HMMSTR
9:30Peter SchattnerTracking Down Non-coding RNAs: The Oher Guide-SnoRNA Genefinder
10:00Igor GrigorievRemote homology detection by CRISSP: Application to protein kinases
10:30Coffee
11:00Bob EdgarImproved alignments through profile-profile HMM methods
11:30Jahnavi C. PrasadAutomated Consensus Method of Alignment for Confident Comparative Modeling
12:00Lunch
1:30OPEN
2:00Mark Akeson Nanopores
2:30Coffee
3:00Martin MaderaHave sequence comparison methods reached their full potential?
3:30David JuanAssessing Protein-Protein Interactions in E. coli using information from literature
4:00Thomas Huber High throughput fold determination: Algorithms and computational implementation