binding sites may be used for predicting DNA-binding sites from the structural and even sequence properties of unbound proteins. This approach has been successfully...

effectors. Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes...

prediction software Gene prediction Macromolecular docking Protein–DNA interaction site predictor Two-hybrid screening FastContact Dandekar T., Snel B.,Huynen...

DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins...

compacting structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed. DNA is a long polymer made...

also known as protein–protein interactions, PPIs; or between small molecules and proteins) but can also describe sets of indirect interactions among genes...

acceptor site affect splice site selection. Also, point mutations in the underlying DNA or errors during transcription can activate a cryptic splice site in...

essential roles in DNA repair. Variants such as H2A.X are phosphorylated at sites of DNA damage, marking regions for recruitment of repair proteins. This modification...

of a DNA sequence (e.g. a genome) and (2) they are bound by DNA-binding proteins. DNA binding sites are often associated with specialized proteins known...

2007). "Dynamic in vivo interaction of DDB2 E3 ubiquitin ligase with UV-damaged DNA is independent of damage-recognition protein XPC". Journal of Cell Science...

influence of short-range interactions on protein onformation. II. A model for predicting the alpha-helical regions of proteins". Proceedings of the National...

between E3L and the Z-DNA. Overall, these results show that decreasing the bonds and interactions between Z-DNA and Z-DNA binding proteins decreases both virulence...

pattern of interactions of zinc fingers with DNA. The binding of zinc finger is found to be distinct from many other DNA-binding proteins that bind DNA through...

(PPI), protein-peptide interactions, protein-ligand interactions (PLI), and protein-DNA interaction. Calculating contacts is an important task in structural...

epigenetic modification at the site in question. The engineered proteins used for epigenome editing are composed of a DNA binding domain that target specific...

conserved, even within the order of Primates. BEND2 is predicted to be a DNA-binding protein due to the presence of BEN domains at its C-terminus, a...

A; Weirauch, MT; Frey, BJ (Aug 2015). "Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning". Nat Biotechnol. 33 (8):...

disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners...

"UV-induced DNA incision and proliferating cell nuclear antigen recruitment to repair sites occur independently of p53-replication protein A interaction in p53...

database of DNA variations in putative microRNA target sites PolyQ: database of polyglutamine repeats in disease and non-disease associated proteins Rfam: a...

type of interaction was not studied yet. The interactions with PNN, OTUD68, and ACTR6 were predicted by co-expression. Orthologs of C12orf29 protein are found...

and physics. Protein-protein interaction networks (PINs) represent the physical relationship among proteins present in a cell, where proteins are nodes,...

Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical...

postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Bacteria also use DNA adenine methylation (rather than DNA cytosine methylation)...

shock protein 90) is a chaperone protein that assists other proteins to fold properly, stabilizes proteins against heat stress, and aids in protein degradation...

groove and minor groove, many proteins which bind to B-DNA do so through the wider major groove. The double-helix model of DNA structure was first published...

technology typically used to validate protein interactions. It is based on the association of fluorescent protein fragments that are attached to components...

glycan–protein (protein–glycan) interactions occur between glycans and proteins that they are covalently attached to. Together with protein–protein interactions...

structure forms a large central cavity in which the unfolded protein binds via hydrophobic interactions. This structure is typically in equilibrium with each...

for protein translation. In the context of gene finding, the start-stop definition of an ORF therefore only applies to spliced mRNAs, not genomic DNA, since...