mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures
Open accessAbstract
Computational methods have traditionally struggled to predict the effect of mutations in antibody-antigen complexes on binding affinity. This has limited their usefulness during antibody engineering and development, and their ability to predict biologically relevant escape mutations. Here we present mCSM-AB, a user-friendly web server for accurately predicting antibody-antigen affinity changes upon mutation which relies on graph-based signatures. We show that mCSM-AB performs better than comparable methods that have been previously used for antibody engineering. mCSM-AB web server is available at http://structure.bioc.cam.ac.uk/mcsm_ab.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The graph-based signatures concept has proven to be a powerful approach and has been widely applied to the study of protein structure, including how mutations alter protein stability, dynamics and interactions with other molecules.
“Our previously described graph-based signatures concept has proven to be a powerful approach and has been widely applied to the study of protein structure, including how mutations alter protein stability (20,26), dynamics (27) and interactions with other molecules (20,28–34).”
From mCSM-PPI2: predicting the effects of mutations on protein–protein interactions (2019) · cites this paper as [33]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Comparative Protein Modelling by Satisfaction of Spatial Restraints
Šali, A., & Blundell, T. L. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1626 · Cited by 12,977 · see citing works
Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b00104 · Cited by 5,995 · see citing works
Self-citationThe FoldX web server: an online force field
Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki387 · Cited by 2,759 · see citing works
Sikweyiya, Y. M., & Jewkes, R. K. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035495 · Cited by 1,315 · see citing works
mCSM: Predicting the effects of mutations in proteins using graph-based signatures
Pires, D. E. V., Ascher, D. B., & Blundell, T. L. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt691 · Cited by 1,066 · see citing works
Self-citationPires, D. E. V., Ascher, D. B., & Blundell, T. L. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku411 · Cited by 932 · see citing works
Self-citationReproducibility crisis: Blame it on the antibodies
Baker, M. (2015) · Nature · doi:10.1038/521274a · Cited by 830 · see citing works
Kortemme, T., Morozov, A. V., & Baker, D. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00021-4 · Cited by 516 · see citing works
Specific interactions for ab initio folding of protein terminal regions with secondary structures
Yang, Y., & Zhou, Y. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21968 · Cited by 245 · see citing works
Mechanism of Neutralization by the Broadly Neutralizing HIV-1 Monoclonal Antibody VRC01
Li, Y., O'Dell, S., Walker, L. M., Wu, X., Guenaga, J., Feng, Y., Schmidt, S. D., McKee, K., Louder, M. K., Ledgerwood, J. E., et al. (2011) · Journal of Virology · doi:10.1128/jvi.00754-11 · Cited by 235 · see citing works
Predicting free energy changes using structural ensembles
Benedix, A., Becker, C. M., de Groot, B. L., Caflisch, A., & Böckmann, R. A. (2009) · Nature Methods · doi:10.1038/nmeth0109-3 · Cited by 234 · see citing works
<scp>AB</scp> ‐Bind: Antibody binding mutational database for computational affinity predictions
Sirin, S., Apgar, J. R., Bennett, E. M., & Keating, A. E. (2016) · Protein Science · doi:10.1002/pro.2829 · Cited by 179 · see citing works
Flexibility and small pockets at protein–protein interfaces: New insights into druggability
Jubb, H. C., Blundell, T. L., & Ascher, D. B. (2015) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2015.01.009 · Cited by 154 · see citing works
Self-citationAssessing predictors of changes in protein stability upon mutation using self-consistency
Thiltgen, G., & Goldstein, R. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046084 · Cited by 110 · see citing works
Nemethova, M., Radvánszky, J., Kádaši, Ľ., et al. (2015) · European Journal of Human Genetics · doi:10.1038/ejhg.2015.60 · Cited by 102 · see citing works
Pires, D. E. V., Chen, J., Blundell, T. L., & Ascher, D. B. (2016) · Scientific Reports · doi:10.1038/srep19848 · Cited by 102 · see citing works
Self-citationGermline Mutations in the CDKN2B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma
Jafri, M., Wake, N. C., Ascher, D. B., Pires, D. E. V., Gentle, D., Morris, M. R., Rattenberry, E., Simpson, M. A., Trembath, R. C., Weber, A. P., et al. (2015) · Cancer Discovery · doi:10.1158/2159-8290.cd-14-1096 · Cited by 95 · see citing works
Self-citationPires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku966 · Cited by 91 · see citing works
Self-citationSpassov, V. Z., & Yan, L. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24230 · Cited by 85 · see citing works
Do current therapeutic anti-Aβ antibodies for Alzheimer’s disease engage the target?
Watt, A. D., Crespi, G. A. N., Down, R. A., Ascher, D. B., Gunn, A. P., Perez, K. A., McLean, C., Villemagne, V. L., Parker, M. W., Barnham, K. J., et al. (2014) · Acta Neuropathologica · doi:10.1007/s00401-014-1290-2 · Cited by 60 · see citing works
Self-citationUsher, J. L., Ascher, D. B., Pires, D. E. V., et al. (2014) · JIMD Reports · doi:10.1007/8904_2014_380 · Cited by 56 · see citing works
Self-citationChan, L. J., Bulitta, J. B., Ascher, D. B., Haynes, J. M., McLeod, V. M., Porter, C. J. H., Williams, C. C., & Kaminskas, L. M. (2015) · Molecular Pharmaceutics · doi:10.1021/mp5006189 · Cited by 39 · see citing works
Self-citationProtein-Protein Interactions: Structures and Druggability
Ascher, D. B., Jubb, H. C., Pires, D. E. V., Ochi, T., Higueruelo, A. P., & Blundell, T. L. (2015) · NATO science for peace and security series. A, Chemistry and biology · doi:10.1007/978-94-017-9719-1_12 · Cited by 13 · see citing works
Self-citationCrespi, G. A. N., Ascher, D. B., Parker, M. W., & Miles, L. A. (2014) · Acta Crystallographica Section F Structural Biology Communications · doi:10.1107/s2053230x14001642 · Cited by 13 · see citing works
Self-citationWun, K. S., Miles, L. A., Crespi, G. A. N., Wycherley, K., Ascher, D. B., Barnham, K. J., Cappai, R., Beyreuther, K. T., Masters, C. L., Parker, M. W., et al. (2008) · Acta Crystallographica Section F Structural Biology and Crystallization Communications · doi:10.1107/s1744309108011718 · Cited by 12 · see citing works
Self-citationNovel Therapeutic Approaches to Treat Alzheimer’s Disease and Memory Disorders
Ascher, D. B., Crespi, G. A. N., Ng, H. L., Morton, C. J., Parker, M. W., & Miles, L. A. (2008) · Journal of Proteomics & Bioinformatics · doi:10.4172/jpb.1000054 · Cited by 6 · see citing works
Self-citationAnti-Aβ antibody target engagement: a response to Siemers et al.
Watt, A. D., Crespi, G. A. N., Down, R. A., Ascher, D. B., Gunn, A. P., Perez, K. A., McLean, C., Villemagne, V. L., Parker, M. W., Barnham, K. J., et al. (2014) · Acta Neuropathologica · doi:10.1007/s00401-014-1333-8 · Cited by 4 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Artificial intelligence to deep learning: machine intelligence approach for drug discovery
Gupta, R., Srivastava, D., Sahu, M., Tiwari, S., Ambasta, R. K., & Kumar, P. (2021) · Molecular Diversity · doi:10.1007/s11030-021-10217-3 · Cited by 1,473 · see citing works
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability
Rodrigues, C. H., Pires, D. E., & Ascher, D. B. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky300 · Cited by 1,086 · see citing works
Self-citationmCSM-PPI2: predicting the effects of mutations on protein–protein interactions
Rodrigues, C. H. M., Myung, Y., Pires, D. E. V., & Ascher, D. B. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz383 · Cited by 369 · see citing works
Self-citationWang, M., Cang, Z., & Wei, G.-W. (2020) · Nature Machine Intelligence · doi:10.1038/s42256-020-0149-6 · Cited by 202 · see citing works
Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2016) · Scientific Reports · doi:10.1038/srep29575 · Cited by 143 · see citing works
Self-citationDeep geometric representations for modeling effects of mutations on protein-protein binding affinity
Liu, X., Luo, Y., Li, P., Song, S., & Peng, J. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009284 · Cited by 140 · see citing works
mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions
Pires, D. E. V., & Ascher, D. B. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx236 · Cited by 127 · see citing works
Self-citationBagchi, A., Haidar, J. N., Eastman, S. W., Vieth, M., Topper, M., Iacolina, M. D., Walker, J. M., Forest, A., Shen, Y., Novosiadly, R. D., et al. (2018) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-17-0575 · Cited by 60 · see citing works
Kinact: a computational approach for predicting activating missense mutations in protein kinases
Rodrigues, C. H., Ascher, D. B., & Pires, D. E. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky375 · Cited by 31 · see citing works
Self-citationAntibody affinity maturation by computational design
Kuroda, D., & Tsumoto, K. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8648-4_2 · Cited by 26 · see citing works
- Authors
- Pires, D. E. V., & Ascher, D. B.
- Affiliations
- Fiocruz Minas (BR)
- The University of Melbourne (AU)
- Corresponding author
- Pires, Douglas E.V.
- Ascher, David B.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-05-23
- Volume
- 44
- Issue
- W1
- Pages
- W469-W473
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4987957
- OpenAlex
- W2400041270
- Cited by
- 134
- References
- 27
- Citations by year
- 2026: 10 · 2025: 15 · 2024: 14 · 2023: 20 · 2022: 15 · 2021: 15 · 2020: 15 · 2019: 12 · 2018: 4 · 2017: 10 · 2016: 4
- FWCI
- 5.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- Arca - Repositório Institucional da Fiocruz (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- Massachusetts Institute of Technology
- Research Councils UK
- Fundação de Amparo à Pesquisa do Estado de Minas Gerais (MR/M026302/1)
- Fundação Oswaldo Cruz
- Conselho Nacional das Fundações Estaduais de Amparo à Pesquisa
- Medical Research Council (MR/M026302/1)
- National Health and Medical Research Council (1072476)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- antibody affinity, mutation effect prediction, antibody engineering, escape mutations, web server, protein-protein complex
- MeSH terms
- Antibodies, Antibody Affinity, Antigen-Antibody Complex, Antigens, Mutation, Software, Vaccines, Protein Engineering, HIV Antibodies, Benchmarking, Internet, Datasets as Topic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
