{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T14:47:06Z","timestamp":1768488426626,"version":"3.49.0"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein\u2013protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required. Here we investigate whether applying coarse-grained (CG) molecular dynamics simulations is a viable alternative for complexes of known structure.<\/jats:p><jats:p>Results: We calculate the free energy barrier with respect to the bound state based on molecular dynamics simulations using both a full atomistic and a CG force field for the TCR\u2013pMHC complex and the MP1\u2013p14 scaffolding complex. We find that the free energy barriers from the CG simulations are of similar accuracy as those from the full atomistic ones, while achieving a speedup of &amp;gt;500-fold. We also observe that extensive sampling is extremely important to obtain accurate free energy barriers, which is only within reach for the CG models. Finally, we show that the CG model preserves biological relevance of the interactions: (i) we observe a strong correlation between evolutionary likelihood of mutations and the impact on the free energy barrier with respect to the bound state; and (ii) we confirm the dominant role of the interface core in these interactions. Therefore, our results suggest that CG molecular simulations can realistically be used for the accurate prediction of protein\u2013protein interaction strength.<\/jats:p><jats:p>Availability and implementation: The python analysis framework and data files are available for download at http:\/\/www.ibi.vu.nl\/downloads\/bioinformatics-2013-btt675.tgz.<\/jats:p><jats:p>Contact: k.a.feenstra@vu.nl<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt675","type":"journal-article","created":{"date-parts":[[2013,11,23]],"date-time":"2013-11-23T03:29:55Z","timestamp":1385177395000},"page":"326-334","source":"Crossref","is-referenced-by-count":47,"title":["Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins"],"prefix":"10.1093","volume":"30","author":[{"given":"Ali","family":"May","sequence":"first","affiliation":[{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"}]},{"given":"Ren\u00e9","family":"Pool","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"}]},{"given":"Erik","family":"van Dijk","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"}]},{"given":"Jochem","family":"Bijlard","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"}]},{"given":"Sanne","family":"Abeln","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"}]},{"given":"Jaap","family":"Heringa","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"}]},{"given":"K. Anton","family":"Feenstra","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, 2Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, 3Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, 4Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and 5Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2013,11,22]]},"reference":[{"key":"2023012710410274500_btt675-B1","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","article-title":"Molecular dynamics with coupling to an external bath","volume":"81","author":"Berendsen","year":"1984","journal-title":"J. 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