Canonical structures for the hypervariable regions of immunoglobulins.

By Cyrus Chothia, Arthur M. Lesk. 1987

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Citations in the corpus

SWISS-MODEL: homology modelling of protein structures and complexes (2018, neutral): “If a matching sequence signal is detected, data can be sent to the Prediction of Immunoglobulin Structure server PIGSPro (44–46) where the model of the antibody is generated according to the canonical structure method (47–49).”
IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. (2003, background): “This numbering, set up after aligning more than 5000 sequences, takes into account and combines the definition of the framework (FR) and complementarity determining regions (CDR) [7], structural data from X-ray diffraction studies [8], and the characterization of the hypervariable loops [9].”
SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models (2010, background): “In our experience with the RosettaAntibody Server [28], there are antibodies with non-H3 loops which elude the traditional Chothia classification system [ 4 ] and may not fit into canonical CDR templates.”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “…search approaches that scan a database of all known protein structures to find segments fitting the anchor core regions (Jones and Thirup, 1986; Chothia and Lesk, 1987); (ii) conformational search approaches that rely on optimizing a scoring function (Moult and James, 1986; Bruccoleri and…”
Antibody Structure and Function: The Basis for Engineering Therapeutics (2019, background): “By analyzing the first crystal structures of Fabs, Chothia and Lesk [31] proposed a definition based on the conserved conformations of the antigen-binding loops named canonical structures.”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “…search approaches that scan a database of all known protein structures to ﬁnd segments ﬁtting the anchor core regions (Jones and Thirup, 1986; Chothia and Lesk, 1987); (ii) conformational search approaches that rely on optimizing a scoring function (Moult and James, 1986; Bruccoleri and…”
Comparative Protein Structure Modeling Using Modeller (2006, methodology): “…search approaches that scan a database of all known protein structures to find segments fitting the anchor core regions (Jones and Thirup, 1986; Chothia and Lesk, 1987); (ii) conformational search approaches that rely on optimizing a scoring function (Moult and James, 1986; Bruccoleri and…”
Comparative Protein Structure Modeling Using MODELLER (2007, methodology): “…search approaches that scan a database of all known protein structures to ﬁnd segments ﬁtting the anchor core regions (Jones and Thirup, 1986; Chothia and Lesk, 1987); (ii) conformational search approaches that rely on optimizing a scoring function (Moult and James, 1986; Bruccoleri and…”
Five computational developability guidelines for therapeutic antibody profiling (2019, background): “In natural antibodies, all CDR loops, apart from CDRH3, are thought to fall into structural classes known as canonical forms (28, 29).”
AbDesign: an algorithm for combinatorial backbone design guided by natural conformations and sequences (2015, methodology): “21,22,25–27,30,47,80–84 Our preliminary in silico experiments using such stem choices, however, resulted in structurally unrealistic designed antibodies with poor packing between the CDR and the framework sidechains.”
OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding. (2010, background): “It is well established that for all CDRs, except H3, there are discrete sets of conformations that their secondary structures assume, known as canonical structures (Chothia and Lesk, 1987).”
A new clustering of antibody CDR loop conformations (2010, background): “For two dihedral angles, θ1 and θ2, of the same type and at the same residue position of two different structures, the distance between them is defined to be: [1]”
Antibody modeling using the Prediction of ImmunoGlobulin Structure (PIGS) web server (2014, methodology): “For the leave-one-out procedure, we did not exclude any putative of Chothia and Lesk 24 .”