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» Sequence variation in ligand binding sites in proteins
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BMCBI
2004
117views more  BMCBI 2004»
13 years 7 months ago
CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting
Background: All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome...
Henry R. Bigelow, Adam S. Wenick, Allan Wong, Oliv...
BMCBI
2007
154views more  BMCBI 2007»
13 years 7 months ago
PepBank - a database of peptides based on sequence text mining and public peptide data sources
Background: Peptides are important molecules with diverse biological functions and biomedical uses. To date, there does not exist a single, searchable archive for peptide sequence...
Timur Shtatland, Daniel Guettler, Misha Kossodo, M...
BMCBI
2006
129views more  BMCBI 2006»
13 years 7 months ago
BIPAD: A web server for modeling bipartite sequence elements
Background: Many dimeric protein complexes bind cooperatively to families of bipartite nucleic acid sequence elements, which consist of pairs of conserved half-site sequences sepa...
Chengpeng Bi, Peter K. Rogan
BMCBI
2004
207views more  BMCBI 2004»
13 years 7 months ago
Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resen
Background: Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition moti...
Davide Corà, Ferdinando Di Cunto, Paolo Pro...
BMCBI
2010
167views more  BMCBI 2010»
13 years 7 months ago
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies
Background: Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription fa...
Denitsa Alamanova, Philip Stegmaier, Alexander E. ...