UniProt - annotated protein sequence database TRANSFAC - transcription factor database RegulonDB - a database on transcriptional regulation and genome organization E. coli genome project GenProtEC - E. coli genome and proteome database EcoCyc - encyclopedia of E. coli genes and metabolism E. coli promoters - experimentally identified transcriptional start sites E. coli transcription factor binding sites - transcription factor binding site predictions in the E. coli genome made by cross-species comparison
Protein and DNA structure
PDB - Protein Data Bank, a repository for the processing and distribution of 3-D biological macromolecular structure data NDB - Nucleic Acid Database, a repository of three-dimensional structural information about nucleic acids
DNA-protein interaction
DPInteract - a database on protein-DNA interactions ProNIT - thermodynamic database for protein-nucleic acid interactions
Molecular Biomechanics Labs
Bustamante Group - single-molecule manipulation studies of the dynamics, structure and kinetics of molecular motors and nucleo-protein assemblies Crothers Lab - relation between DNA bending and its function, RNA conformation Richard Ebright - understanding of the structure, function, and regulation of transcription initiation complexes, and to develop gene-specific inhibitors of transcription initiation as potential gene-specific therapeutic agents. Gerstein Lab - research on comparative genomics, mining expression datasets, macromolecular motions Robert Jernigan - theoretical studies on the structures of proteins, nucleic acids, and small molecules, and on their interactions; study of large motion of proteins Kahn Lab - use of designed or random DNA molecules with intrinsic curvature to investigate protein-DNA conformation or nucleic acid structure and dynamics. Ned Seeman's Lab - DNA nanotechnology Alex Vologodskii - large-scale conformational properties of double-helical DNA