Absence of a simple code: how transcription factors read the genome
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
Origins of specificity in protein-DNA recognition
Specific interactions between proteins and DNA are fundamental to many biological
processes. In this review, we provide a revised view of protein-DNA interactions that …
processes. In this review, we provide a revised view of protein-DNA interactions that …
Protein–DNA binding: complexities and multi-protein codes
Binding of proteins to particular DNA sites across the genome is a primary determinant of
specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded …
specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded …
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments
Here, a scalable, accurate, reliable, and robust protein functional site comparison algorithm
is presented. The key components of the algorithm consist of a reduced representation of the …
is presented. The key components of the algorithm consist of a reduced representation of the …
Kernel-based machine learning protocol for predicting DNA-binding proteins
N Bhardwaj, RE Langlois, G Zhao… - Nucleic Acids Research, 2005 - academic.oup.com
DNA-binding proteins (DNA-BPs) play a pivotal role in various intra-and extra-cellular
activities ranging from DNA replication to gene expression control. Attempts have been …
activities ranging from DNA replication to gene expression control. Attempts have been …
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
Structural and physical properties of DNA provide important constraints on the binding sites
formed on surfaces of DNA-targeting proteins. Characteristics of such binding sites may form …
formed on surfaces of DNA-targeting proteins. Characteristics of such binding sites may form …
Nuance in the double-helix and its role in protein–DNA recognition
It has been known for some time that the double-helix is not a uniform structure but rather
exhibits sequence-specific variations that, combined with base-specific intermolecular …
exhibits sequence-specific variations that, combined with base-specific intermolecular …
Biomacromolecular quantitative structure–activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein–protein …
Quantitative structure–activity relationship (QSAR), a regression modeling methodology that
establishes statistical correlation between structure feature and apparent behavior for a …
establishes statistical correlation between structure feature and apparent behavior for a …
A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug …
Functional relationships between proteins that do not share global structure similarity can be
established by detecting their ligand-binding-site similarity. For a large-scale comparison, it …
established by detecting their ligand-binding-site similarity. For a large-scale comparison, it …
Insights into protein–DNA interactions through structure network analysis
R Sathyapriya, MS Vijayabaskar… - PLoS computational …, 2008 - journals.plos.org
Protein–DNA interactions are crucial for many cellular processes. Now with the increased
availability of structures of protein–DNA complexes, gaining deeper insights into the nature …
availability of structures of protein–DNA complexes, gaining deeper insights into the nature …