Selection of DNA binding sites by regulatory proteins
|
journal
|
February 1987 |
MatInspector and beyond: promoter analysis based on transcription factor binding sites
|
journal
|
April 2005 |
A Biophysical Approach to Transcription Factor Binding Site Discovery
|
journal
|
November 2003 |
MATCHTM: a tool for searching transcription factor binding sites in DNA sequences
|
journal
|
July 2003 |
Comparative analysis of methods for representing and searching for transcription factor binding sites
|
journal
|
August 2004 |
Matlnd and Matlnspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data
|
journal
|
January 1995 |
DNA binding sites: representation and discovery
|
journal
|
January 2000 |
Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
|
journal
|
June 2005 |
Toward an atomistic model for predicting transcription-factor binding sites
|
journal
|
June 2004 |
Protein-DNA binding specificity predictions with structural models
|
journal
|
October 2005 |
Connecting protein structure with predictions of regulatory sites
|
journal
|
April 2007 |
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors
|
journal
|
March 2009 |
Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
|
journal
|
May 2008 |
A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors
|
journal
|
January 2007 |
Protein-DNA Recognition Patterns and Predictions
|
journal
|
June 2005 |
Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials
|
journal
|
October 2006 |
Predicting indirect readout effects in protein-DNA interactions
|
journal
|
May 2004 |
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition
|
journal
|
July 2006 |
Intermolecular and Intramolecular Readout Mechanisms in Protein–DNA Recognition
|
journal
|
March 2004 |
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
|
journal
|
December 2007 |
Chromatin Immunoprecipitation for Determining the Association of Proteins with Specific Genomic Sequences In Vivo
|
journal
|
June 2004 |
Simulation and modeling of nucleic acid structure, dynamics and interactions
|
journal
|
June 2004 |
Recent advances in the study of nucleic acid flexibility by molecular dynamics
|
journal
|
April 2008 |
Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(CpG) Steps
|
journal
|
December 2004 |
Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps
|
journal
|
December 2005 |
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
|
journal
|
November 2009 |
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
|
journal
|
September 1992 |
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
|
journal
|
September 2003 |
Scalable molecular dynamics with NAMD
|
journal
|
January 2005 |
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
|
journal
|
January 2000 |
A standard reference frame for the description of nucleic acid base-pair geometry 1 1Edited by P. E. Wright 2 2This is a document of the Nomenclature Committee of IUBMB (NC-IUBMB)/IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN), whose members are R. Cammack (chairman), A. Bairoch, H.M. Berman, S. Boyce, C.R. Cantor, K. Elliott, D. Horton, M. Kanehisa, A. Kotyk, G.P. Moss, N. Sharon and K.F. Tipton.
|
journal
|
October 2001 |
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
|
journal
|
July 1985 |
From genomics to chemical genomics: new developments in KEGG
|
journal
|
January 2006 |
A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome 1 1Edited by R. Ebright
|
journal
|
November 1998 |
An introduction to ROC analysis
|
journal
|
June 2006 |
Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/GcvR interaction and allow GcvA-mediated activation of the Escherichia coli gcvTHP operon
|
journal
|
July 2002 |
Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA
|
journal
|
May 2000 |
Additivity in protein-DNA interactions: how good an approximation is it?
|
journal
|
October 2002 |
The shape of the DNA minor groove directs binding by the DNA-bending protein Fis
|
journal
|
April 2010 |
Probabilistic Code for DNA Recognition by Proteins of the EGR Family
|
journal
|
November 2002 |
Design Principles for Regulator Gene Expression in a Repressible Gene Circuit
|
journal
|
September 2003 |
Simulation and modeling of nucleic acid structure, dynamics and interactions
|
journal
|
May 2004 |
MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices
|
journal
|
January 1995 |