Antibodies have the capacity to bind a diverse set of antigens, and they have become critical therapeutics and diagnostic molecules. The binding of antibodies is facilitated by a set of six hypervariable loops that are diversified through genetic recombination and mutation. Even with recent advances,...
Three-dimensional structures of the antibody-antigen complexes are useful for understanding their mechanism and for designing improved antibody drugs. Experimental determination of structures is laborious and not always possible, so I have developed computational tools to predict the structures of antibody ...
Machine learning (ML) is a key technology for accurate prediction of antibody–antigen binding. Two orthogonal problems hinder the application of ML to antibody-specificity prediction and the benchmarking thereof: the lack of a unified ML formalization of immunological antibody-specificity prediction prob...
Abadapt: an adaptive approach to predicting antibody–antigen complex structures from sequence Bioinformatics Advances, 2 (2022), Article vbac015 View in ScopusGoogle Scholar 17 M.L. Fernández-Quintero, A. Vangone, J.R. Loeffler, C.A. Seidler, G. Georges, K.R. Liedl Paratope states in ...
Comparative analysis of nanobody sequence and structure data 2018, Proteins: Structure, Function and Bioinformatics BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes 2017, Nucleic Acids Research ANARCI: Antigen receptor numbering and receptor classification 2016, Bi...
The OptCDR method [32] addresses the de novo design of the antigen binding regions, known as complementarity determining regions (CDR), of an antibody to bind any specified epitope of an antigen. However, CDR only capture part of the binding capacity of an antibody and are not constrained ...
strpred.yml Sample only the structure of one CDR (structure prediction). Antibody-Antigen Complex Below is the usage of design_pdb.py. It samples CDRs for antibody-antigen complexes. The full list of options can be found in diffab/tools/runner/design_for_pdb.py. python design_pdb.py \ ...
蛋白别名:B-cell activation marker; BCM1 surface antigen; BLAST-1; CD48; CD48 antigen; CD48 antigen (B cell membrane protein); CD48d; HM48-1; MRC OX-45 surface antigen; sCD 48; sCD48; sgp-60; Signaling lymphocytic activation molecule 2; Signaling lymphocytic activation molecule 2 (SLAM...
diversity of the generated sequences and their similarity to natural sequences. Additionally, we employed the SOTA antibody-antigen complex structure prediction method, tFold47, to generate complexes between the modeled antibodies and the target antigen, following the benchmark protocol. We then ...
requires the three-dimensional structure of the antigen–antibody complex. However, antibody-antigen complexes are easier to crystalize than monomers because the complexes are normally stable23. In addition, complex structures can be predicted using homology modeling24,25and docking simulation26. In this...