Structural and physical properties of DNA provide important constraints on the binding sites formed on surfaces of

DNA-binding protein DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for DNA#Base pairing, single- or double-stranded DNA. Sequence-specific DNA-binding proteins generally interact with the major groove ...

s. Characteristics of such

binding sites In biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. The binding partner of the macromolecule is often referred to as a ligand. Ligands may inclu ...

may be used for predicting DNA-binding sites from the

structural A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such a ...

and even

sequence In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is calle ...

properties of unbound proteins. This approach has been successfully implemented for predicting the protein–protein interface. Here, this approach is adopted for predicting DNA-binding sites in DNA-binding proteins. First attempt to use sequence and evolutionary features to predict DNA-binding sites in proteins was made by Ahmad et al. (2004) and Ahmad and Sarai (2005). Some methods use structural information to predict DNA-binding sites and therefore require a three-dimensional structure of the protein, while others use only sequence information and do not require protein structure in order to make a prediction.

Web servers

Structure- and sequence-based prediction of DNA-binding sites in DNA-binding proteins can be performed on several web servers listed below. DISIS predicts DNA binding sites directly from the

amino acid sequence Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthes ...

and hence is applicable for all known proteins. It is based on the chemical-physical properties of the residue and its environment, predicted structural features and evolutionary data. It uses

machine learning Machine learning (ML) is a field of inquiry devoted to understanding and building methods that 'learn', that is, methods that leverage data to improve performance on some set of tasks. It is seen as a part of artificial intelligence. Machine ...

algorithms. DISIS2 receives the raw amino acid sequence and generates all features from it, such as

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

, solvent accessibility, disorder, b-value, protein-protein interaction,

coiled coil A coiled coil is a structural motif in proteins in which 2–7 alpha-helices are coiled together like the strands of a rope. (Dimers and trimers are the most common types.) Many coiled coil-type proteins are involved in important biological fun ...

s, and

evolutionary profile Phylogenetic profiling is a bioinformatics technique in which the joint presence or joint absence of two traits across large numbers of species is used to infer a meaningful biological connection, such as involvement of two different proteins in the ...

s, etc. The amount of predicted features is much larger than of DISIS (previous version). Finally, DISIS2 is able to predict DNA-binding residues from protein sequence of DNA-binding proteins. DNABindR predicts DNA binding sites from amino acid sequences using machine learning algorithms.Yan, C., Terribilini, M., Wu, F., Jernigan, R.L., Dobbs, D., and Honavar V. Predicting DNA-binding sites of proteins from amino acid sequence.

BMC Bioinformatics ''BMC Bioinformatics'' is a peer-reviewed open access scientific journal covering bioinformatics and computational biology published by BioMed Central. It was established in 2000, and has been one of the fastest growing and most successful journals ...

, 2006, 7:262 DISPLAR makes a prediction based on properties of protein structure. Knowledge of the protein structure is required Tjong , H. and Zhou, H.-X. DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.

Nucleic Acids Research ''Nucleic Acids Research'' is an open-access peer-reviewed scientific journal published since 1974 by the Oxford University Press. The journal covers research on nucleic acids, such as DNA and RNA, and related work. According to the ''Journal Cit ...

35:1465-1477 (2007) BindN makes a prediction based on chemical properties of the input protein sequence. Knowledge of the protein structure is not required.L. Wang, and S. J. Brown. "BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences."

. 2006 Jul 1;34(Web Server issue):W243-8. BindN+ is an upgraded version of BindN that applies

support vector machine In machine learning, support vector machines (SVMs, also support vector networks) are supervised learning models with associated learning algorithms that analyze data for classification and regression analysis. Developed at AT&T Bell Laboratorie ...

s (SVMs) to sequence-based prediction of DNA or RNA-binding residues from biochemical features and evolutionary information.Wang L, Huang C, Yang MQ, Yang JY. "BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features"

BMC Systems Biology ''BMC Systems Biology'' was an open access peer-reviewed scientific journal that covered research in systems biology. Filling a gap in what was a new research field, the journal was established in 2007 and is published by BioMed Central. Part of ...

2010 4(Suppl 1):S3 DP-Bind combines multiple methods to make a consensus prediction based on the profile of evolutionary conservation and properties of the input protein sequence. Profile of evolutionary conservation is automatically generated by the web-server. Knowledge of the protein structure is not required.Hwang, S , Gou, Z and Kuznetsov, I.B. "DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins"

Bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

2007 23(5):634-636 DBS-PSSM(This article also shows how prediction can be significantly sped up by generating alignments against limited data sets) and DBS-Pred (This article also uses amino acid composition analysis to predict DNA-binding proteins, and uses structure information to improve binding site prediction. The method is based on single sequences only and thousands of proteins can be processed in less than an hour). Standalone is also available. predict the DNA-binding in a protein from their sequence information.

References

{{DEFAULTSORT:Protein-DNA interaction site predictor DNA

Web servers

See also

References