Harvard-CMCD-20080505-Nets.ppt

Quo Vadis Structural Biology: Networks, Variation, Flexibility Mark B GersteinYale Comp. Bio. Bioinformatics Quo Vadis, Boston, MA 2008.05.05, 19:00-20:00 Slides downloadable from Lectures.GersteinL  Please read permissions statement. Paper references mostly from Papers.GersteinL. Compact vers. of Networks Talk then Compact Motions Talk: Nets-Intro w.o. names + SIN + Disorder + Netpossel + CD4 + Net-Tools tyna+coev + Brief MolMovDB + HingeAtlas + FlexOracle + HingeMaster ; To get movies to work put contents of zipfile below into same directory as this ppt: /ppt/pfizer-motions-座机电话号码/movies-put-in-same-dir-as-ppt.pfizer-motions-座机电话号码.zip ; Everything fits within 50 min Quo Vadis Structural Biology: Networks, Variation, Flexibility Where to go in computational structural biology: big structures, long simulations….? 1. Mine lots of normal-size structures 2. “Mash-up” structures with “omics” data a. Relating Structures Networks b. Using Structures to Human Variation c. Quantifying Flexibility from Many Structures The problem: Grappling with Function on a Genome Scale? 250 of ~530 originally characterized on chr. 22 [Dunham et al. Nature 1999 ] 25K Proteins in Entire Human Genome with alt. splicing Traditional single molecule way to integrate evidence describe function Some obvious issues in scaling single molecule definition to a genomic scale Fundamental complexities Often 2 proteins/function Multi-functionality: 2 functions/protein Role Conflation: molecular, cellular, phenotypic Some obvious issues in scaling single molecule definition to a genomic scale Fundamental complexities Often 2 proteins/function Multi-functionality: 2 functions/protein Role Conflation: molecular, cellular, phenotypic Fun terms… but do they scale?.... Starry night P Adler, ’94 Naming Pathologies: Related to Single Genes Naming Pathologies:Involving Multiple Gene Names Toward Systematic Ontologies for Function, using Networks Networks