Conformations of the third hypervariable region in the VH domain of immunoglobulins.

By V. Morea, Anna Tramontano, M. Rustici, Cyrus Chothia, Arthur M. Lesk. 1998

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Citations in the corpus

Improving Loop Modeling of the Antibody Complementarity-Determining Region 3 Using Knowledge-Based Restraints (2016, background): “There is a growing body of work surrounding canonical structures of antibody CDR loops, first described by Chothia and colleagues and updated as recently at 2011 by the Dunbrack group [9,10].”
PIGSPro: prediction of immunoGlobulin structures v2 (2017, background): “The region of the loop closer to the framework (named the ‘torso’(16)) follows a canonical structure model and its first four and last six residues form a bulged or non-bulged beta sheet conformation according to the identity of the residues at position 94 and 101 of the heavy chain (Figure 1B)…”
Immunoglobulin Analysis Tool: A Novel Tool for the Analysis of Human and Mouse Heavy and Light Chain Transcripts (2012, background): “IgAT ANALYZES THE LENGTH OF CDR-H3 AND ITS COMPONENTS AND CALCULATES PREDICTIONS FOR STRUCTURAL PROPERTIES OF CDR-H3 The CDR-H3 loop can assume an almost unlimited diversity of differing three dimensional shapes which are grouped into canonical structures (Morea et al., 1998).”
SAbDab: the structural antibody database (2013, background): “The remaining loop, H3, is more variable and cannot be treated in the same way (17).”
A new clustering of antibody CDR loop conformations (2010, unknown): “L3-7A 1 L3-7-1 1DFBL L3-8A 1 L3-8-2 1YQVL L3-8B 1 L3-8-1 1EAPA(14) L3-9A 40 L3-9-cis7-1 1FGVL 1HILA 1IGML 1FVCA 1TETL + 30 more; 1BBDL(25) 1CGSL (30) L3-9-cis7-2 1VFAA(4) 1BBJA(40) L3-9-2 2GFBM(9) L3-9B 1 L3-9-cis6-1 2FBJL L3-9C 2 L3-9-1 1MFAL(23) 7FABL(46)”
Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. (2000, background): “…is encoded by the D and J-minigene segments and uncoded nucleotides (N-region diversity), structural families have been de®ned only very recently (Morea et al., 1998; Oliva et al., 1998), but structural predictions are not approaching the accuracy seen for the canonical folds of the other CDRs.”
Antibody Structure and Function: The Basis for Engineering Therapeutics (2019, background): “In early studies of CDR-H3 structures, the kinked form was more prevalent than the extended one [41].”
Exploiting evolutionary relationships for predicting protein structures (2003, background): “…and a few other family-specific loops, such as antibody hypervariable loops (Al-Lazikani et al., 1997; Chothia and Lesk, 1987; Chothia et al., 1989; Morea et al., 1997, 1998b; Tramontano et al., 1990; Tramontano and Lesk, 1992), have been demonstrated to assume main-chain structures predictable…”
RosettaAntibodyDesign (RAbD): A general framework for computational antibody design (2017, methodology): “Taking advantage of the influx of new structures of antibodies in the PDB, we presented a new clustering of all CDR structures in the Protein Data Bank (PDB) in 2011, updating the Chothia classification developed in the 1980s and 1990s [49–52].”
Structural Bioinformatics (unknown): “As mentioned above, only a partial CS model could be derived for the H3 loop (Al-Lazikani et al., 1997; Morea et al., 1998).”
Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification (2017, methodology): “spanning 95–102 under the Chothia numbering convention (11), the z-score was calculated as , 183”