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Definition
 
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Binding Sites definition: The parts of a macromolecule that directly participate in its specific combination with another molecule.
binding site definition: reactive portion of a macromolecule that directly participates in its specific combination with another molecule.
Binding Sites, Antibody definition: Local surface sites on antibodies which react with antigen determinant sites on antigens. They are formed from parts of the variable regions of FAB FRAGMENTS.
Antibody Binding Site definition: The site at which an antibody makes direct physical contact with a corresponding epitope on an antigen.
 
Examples
 

It was revealed that d(T[ c , s ]T) binds to the central part of the antibody-combining site, while the CPD-flanking nucleotides bind to the positively charged area of the V H domain via electrostatic interactions.

Takuya Torizawa et al.

Nucleic Acids Research 28 (4), 15 Feb 2000

Although the model might simply represent one of the possible multiple conformations at most and not consider any conformational change upon binding to d(T[ c , s ]T), it could at least be concluded that d(T[ c , s ]T) binds the central parts of the antibody-combining site.

Takuya Torizawa et al.

Nucleic Acids Research 28 (4), 15 Feb 2000

Although the 31 P NMR data suggest the existence of a conformational exchange of the CPD-flanking nucleotides on the protein surface ( vide supra ), the residues that exhibit line broadening upon binding to each of the spin-labeled antigens are clustered in a specific area in the V H domain, indicating that the orientations of CPD-containing nucleotides are fairly fixed in the antibody-combining site: both the 3′- and 5′-sides of the flanking deoxynucleotides orient towards the V H domain, as predicted from the chemical shift perturbation data.

Takuya Torizawa et al.

Nucleic Acids Research 28 (4), 15 Feb 2000

On the basis of these data, along with the fact that d(T[ c , s ]T) binds the central parts of the antibody-combining site, we concluded that CPD-containing oligonucleotides bind TDM-2 in a crooked form (a boomerang shape), draping the 3′-side nucleotides onto the H1 and H3 segments and the 5′-side nucleotides onto the H2 and L3 segments.

Takuya Torizawa et al.

Nucleic Acids Research 28 (4), 15 Feb 2000

Tel: +1 847 491 7849; Fax: +1 847 491 4928; Email: t-wu@nwu.edu 1 1 2000 28 1 214 218 23 7 1999 13 10 1999 13 10 1999 Copyright © 2000 Oxford University Press 2000 The Kabat Database was initially started in 1970 to determine the combining site of antibodies based on the available amino acid sequences at that time.

George Johnson et al.

Nucleic Acids Research 28 (1), 01 Jan 2000

1 further example >>
Publications
 

Reactive site polymorphism in the murine protease inhibitor gene family is delineated using a modification of the PCR reaction (PCR + 1).

F Borriello et al.

Nucleic Acids Research , 25 Sep 1990

An in silico approach to map the binding site of doxorubicin on hemoglobin

Shahper Nazeer Khan et al.

Bioinformation , 14 Jul 2008

Domain-based small molecule binding site annotation

Kevin A Snyder et al.

BMC Bioinformatics , 17 Mar 2006

Evolutionary trace analysis at the ligand binding site of laccase

Saharuddin Bin Mohamad et al.

Bioinformation , 18 Jun 2008

Localization of the major ethidium bromide binding site on tRNA.

W C Chu et al.

Nucleic Acids Research , 01 Oct 1997

A high affinity binding site for the HIV-1 nucleocapsid protein.

J A Berglund et al.

Nucleic Acids Research , 01 Mar 1997

Scoring functions for transcription factor binding site prediction

Markus Friberg et al.

BMC Bioinformatics , 04 Apr 2005

A web server for transcription factor binding site prediction

Gang Su et al.

Bioinformation , 15 Jun 2006

POBO, transcription factor binding site verification with bootstrapping

Matti Kankainen et al.

Nucleic Acids Research , 01 Jul 2004

A diminutive and specific RNA binding site for L-tryptophan

Irene Majerfeld et al.

Nucleic Acids Research , 2005

1646 further publications >>