Computational Docking of Antibody-Antigen Complexes, Opportunities and Pitfalls Illustrated by Influenza Hemagglutinin, International Journal of Molecular Sciences, vol.4, issue.1 ,
DOI : 10.1073/pnas.91.6.2358
URL : http://www.mdpi.com/1422-0067/12/1/226/pdf
, , pp.226-251, 2011.
Flexible protein???protein docking, Current Opinion in Structural Biology, vol.16, issue.2, pp.194-200, 2006. ,
DOI : 10.1016/j.sbi.2006.02.002
Updates to the Integrated Protein???Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2, Journal of Molecular Biology, vol.427, issue.19, pp.427-3031, 2015. ,
DOI : 10.1016/j.jmb.2015.07.016
Welcome to CAPRI: A Critical Assessment of PRedicted Interactions, Proteins: Structure, Function, and Genetics, vol.47, issue.3, pp.47-257, 2002. ,
DOI : 10.1002/prot.10111
Classification of protein complexes based on docking difficulty, Proteins: Structure, Function, and Bioinformatics, vol.60, issue.2, 2005. ,
DOI : 10.1002/prot.20554
Docking and scoring protein interactions: CAPRI, Proteins, vol.78, 2009. ,
Antibody Multispecificity Mediated by Conformational Diversity, Science, vol.299, issue.5611, pp.299-1362, 2003. ,
DOI : 10.1126/science.1079731
Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility, Proteins: Structure, Function, and Bioinformatics, vol.348, issue.Database issue, pp.846-858, 2009. ,
DOI : 10.4049/jimmunol.173.1.15
A Systematic Comparison of Free and Bound Antibodies Reveals Binding-Related Conformational Changes, The Journal of Immunology, vol.189, issue.10, pp.4890-4899, 2012. ,
DOI : 10.4049/jimmunol.1201493
Antibody-antigen interactions, Current Opinion in Structural Biology, vol.3, issue.1, pp.113-118, 1993. ,
DOI : 10.1016/0959-440X(93)90210-C
Antibody-antigen interactions: new structures and new conformational changes, Current Opinion in Structural Biology, vol.4, issue.6, pp.857-867, 1994. ,
DOI : 10.1016/0959-440X(94)90267-4
, Biochemistry, vol.39, issue.21, pp.6296-6309, 2000.
DOI : 10.1021/bi000054l
Structural evidence for induced fit as a mechanism for antibody-antigen recognition, Science, vol.255, issue.5047, pp.959-965, 1992. ,
DOI : 10.1126/science.1546293
Local and Transmitted Conformational Changes on Complexation of an Anti-sweetener Fab, Journal of Molecular Biology, vol.236, issue.1, pp.247-274, 1994. ,
DOI : 10.1006/jmbi.1994.1133
An autoantibody to single-stranded DNA: Comparison of the three-dimensional structures of the unliganded fab and a deoxynucleotide-fab complex, Proteins: Structure, Function, and Genetics, vol.23, issue.3, pp.11-159, 1991. ,
DOI : 10.1007/978-1-4612-5190-3
ANARCI: antigen receptor numbering and receptor classification, Bioinformatics, vol.3, 2016. ,
DOI : 10.1016/j.bbapap.2014.07.006
The PyMOL Molecular Graphics System, Version 1, p.20, 2015. ,
Introduction to Protein Structure, 1999. ,
Antibody Elbow Angles are Influenced by their Light Chain Class, Journal of Molecular Biology, vol.357, issue.5, pp.1566-1574, 2006. ,
DOI : 10.1016/j.jmb.2006.01.023
SwarmDock and the Use of Normal Modes in Protein-Protein Docking, International Journal of Molecular Sciences, vol.102, issue.10, pp.3623-3648, 2010. ,
DOI : 10.1021/jp973084f
Detection and refinement of encounter complexes for protein-protein docking: Taking account of macromolecular crowding, Proteins: Structure, Function, and Bioinformatics, vol.8, issue.15, pp.78-3189, 2010. ,
DOI : 10.1002/prot.22770
pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking, Proteins: Structure, Function, and Bioinformatics, vol.101, issue.2, pp.503-515, 2007. ,
DOI : 10.1002/prot.21419
ZDOCK: An initial-stage protein-docking algorithm, Proteins: Structure, Function, and Genetics, vol.162, issue.1, 2003. ,
DOI : 10.1021/bi00113a014
A novel shape complementarity scoring function for protein-protein docking, Proteins: Structure, Function, and Genetics, vol.51, issue.3, p.51, 2003. ,
DOI : 10.1002/prot.10334
HADDOCK:?? A Protein???Protein Docking Approach Based on Biochemical or Biophysical Information, Journal of the American Chemical Society, vol.125, issue.7, pp.1731-1737, 2003. ,
DOI : 10.1021/ja026939x
Canonical structures for the hypervariable regions of immunoglobulins, Journal of Molecular Biology, vol.196, issue.4, pp.901-91710, 1987. ,
DOI : 10.1016/0022-2836(87)90412-8
, Conformations of immunoglobulin hypervariable regions, pp.342-877, 1038.
Standard conformations for the canonical structures of immunoglobulins, J. Mol. Biol, vol.273, 1997. ,
A New Clustering of Antibody CDR Loop Conformations, Journal of Molecular Biology, vol.406, issue.2, pp.228-256, 2011. ,
DOI : 10.1016/j.jmb.2010.10.030
Variable Regions of Antibodies and T-Cell Receptors May Not Be Sufficient in Molecular Simulations Investigating Binding, Journal of Chemical Theory and Computation, vol.13, issue.7, pp.3097-310520, 2017. ,
DOI : 10.1021/acs.jctc.7b00080
, Canonical structures for the hypervariable regions of immunoglobulins, J. Mol. Biol, vol.19687, pp.901-91710, 1987.
, Conformations of immunoglobulin hypervariable regions, pp.342-877, 1038.
Structural Families in Loops of Homologous Proteins: Automatic Classification, Modelling and Application to Antibodies, Journal of Molecular Biology, vol.263, issue.5, pp.800-815, 1996. ,
DOI : 10.1006/jmbi.1996.0617
, uk: Dr. Andrew C.R. Martin's Group at UCL