{"entity": "researcher", "timestamp": "2026-08-22T06:57:28.010Z", "family": "Pudney", "given": "Christopher R", "initials": "CR", "orcid": "0000-0001-6211-0086", "affiliations": ["Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/e46df883c623428aba5d01bcf59c1895.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/e46df883c623428aba5d01bcf59c1895"}}, "publications": [{"entity": "publication", "iuid": "7858c9014b094f75b3cc6bd6595f5398", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7858c9014b094f75b3cc6bd6595f5398.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7858c9014b094f75b3cc6bd6595f5398"}}, "title": "Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA.", "authors": [{"family": "Crean", "given": "Rory M", "initials": "RM"}, {"family": "Pudney", "given": "Christopher R", "initials": "CR", "orcid": "0000-0001-6211-0086", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e46df883c623428aba5d01bcf59c1895.json"}}, {"family": "Cole", "given": "David K", "initials": "DK"}, {"family": "van der Kamp", "given": "Marc W", "initials": "MW", "orcid": "0000-0002-8060-3359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e09f39776374aeca06c0a767d62bfac.json"}}], "type": "journal article", "published": "2022-02-14", "journal": {"title": "J Chem Inf Model", "issn": "1549-960X", "volume": "62", "issue": "3", "pages": "577-590", "issn-l": "1549-9596"}, "abstract": "Accurate and efficient in silico ranking of protein-protein binding affinities is useful for protein design with applications in biological therapeutics. One popular approach to rank binding affinities is to apply the molecular mechanics Poisson-Boltzmann/generalized Born surface area (MMPB/GBSA) method to molecular dynamics (MD) trajectories. Here, we identify protocols that enable the reliable evaluation of T-cell receptor (TCR) variants binding to their target, peptide-human leukocyte antigens (pHLAs). We suggest different protocols for variant sets with a few (\u22644) or many mutations, with entropy corrections important for the latter. We demonstrate how potential outliers could be identified in advance and that just 5-10 replicas of short (4 ns) MD simulations may be sufficient for the reproducible and accurate ranking of TCR variants. The protocols developed here can be applied toward in silico screening during the optimization of therapeutic TCRs, potentially reducing both the cost and time taken for biologic development.", "doi": "10.1021/acs.jcim.1c00765", "pmid": "35049312", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9097153"}], "notes": [], "created": "2026-08-21T11:32:58.073Z", "modified": "2026-08-21T11:32:58.145Z"}, {"entity": "publication", "iuid": "79b28f5d35424275a9aeec9755d5895e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/79b28f5d35424275a9aeec9755d5895e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/79b28f5d35424275a9aeec9755d5895e"}}, "title": "Chemical Mapping Exposes the Importance of Active Site Interactions in Governing the Temperature Dependence of Enzyme Turnover.", "authors": [{"family": "Winter", "given": "Samuel D", "initials": "SD"}, {"family": "Jones", "given": "Hannah B L", "initials": "HBL"}, {"family": "R\u0103s\u0103dean", "given": "Dora M", "initials": "DM"}, {"family": "Crean", "given": "Rory M", "initials": "RM"}, {"family": "Danson", "given": "Michael J", "initials": "MJ"}, {"family": "Panto\u015f", "given": "G Dan", "initials": "GD"}, {"family": "Katona", "given": "Gergely", "initials": "G"}, {"family": "Prentice", "given": "Erica", "initials": "E", "orcid": "0000-0001-7417-7296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c35c332a9b634fc68afcf3c5f8e1b936.json"}}, {"family": "Arcus", "given": "Vickery L", "initials": "VL"}, {"family": "van der Kamp", "given": "Marc W", "initials": "MW", "orcid": "0000-0002-8060-3359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e09f39776374aeca06c0a767d62bfac.json"}}, {"family": "Pudney", "given": "Christopher R", "initials": "CR", "orcid": "0000-0001-6211-0086", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e46df883c623428aba5d01bcf59c1895.json"}}], "type": "journal article", "published": "2021-12-17", "journal": {"title": "ACS Catal", "issn": "2155-5435", "volume": "11", "issue": "24", "pages": "14854-14863", "issn-l": "2155-5435"}, "abstract": "Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, \u0394C P \u2021, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions at the active site can affect long-range protein dynamics and link to enzyme temperature activity. Here, we use a model promiscuous enzyme (glucose dehydrogenase from Sulfolobus solfataricus) to chemically map how individual substrate interactions affect the temperature dependence of enzyme activity and the network of motions throughout the protein. Utilizing a combination of kinetics, red edge excitation shift (REES) spectroscopy, and computational simulation, we explore the complex relationship between enzyme-substrate interactions and the global dynamics of the protein. We find that changes in \u0394C P \u2021 and protein dynamics can be mapped to specific substrate-enzyme interactions. Our study reveals how subtle changes in substrate binding affect global changes in motion and flexibility extending throughout the protein.", "doi": "10.1021/acscatal.1c04679", "pmid": "34956689", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8689651"}], "notes": [], "created": "2026-08-20T08:08:59.537Z", "modified": "2026-08-21T11:35:08.836Z"}, {"entity": "publication", "iuid": "bac40f71ba3d42d591963ca971039c48", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bac40f71ba3d42d591963ca971039c48.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bac40f71ba3d42d591963ca971039c48"}}, "title": "Chemical mapping exposes the importance of active site interactions in governing the temperature dependence of enzyme turnover", "authors": [{"family": "Winter", "given": "SD", "initials": "S"}, {"family": "Jones", "given": "HBL", "initials": "H"}, {"family": "R\u0103s\u0103dean", "given": "DM", "initials": "D"}, {"family": "Crean", "given": "RM", "initials": "R"}, {"family": "Danson", "given": "MJ", "initials": "M"}, {"family": "Panto\u015f", "given": "GD", "initials": "G"}, {"family": "Katona", "given": "G", "initials": "G", "orcid": "0000-0002-2031-8716", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c4b212c300f484ca144993ef6ae9a3c.json"}}, {"family": "Prentice", "given": "E", "initials": "E"}, {"family": "Arcus", "given": "VL", "initials": "V"}, {"family": "van der Kamp", "given": "MW", "initials": "M"}, {"family": "Pudney", "given": "CR", "initials": "C", "orcid": "0000-0001-6211-0086", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e46df883c623428aba5d01bcf59c1895.json"}}], "type": "posted-content", "published": "2021-06-25", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.06.25.449875", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:05:15.506Z", "modified": "2026-08-20T10:05:15.614Z"}]}