From large conformational changes in proteins to environmental bias corrections

Funding Information: This work was granted access to the HPC resources of IDRIS and TGCC under the allocations 2022-A0120713456 (P.C.T.S) and 2023-A0140713456 (P.C.T.S.) made by GENCI. We also acknowledge the support of the Center Blaise Pascal\u2019s IT test platform at ENS de Lyon (Lyon, France) for the computer facilities. The platform operates the SIDUS solution developed by Emmanuel Quemener123. We thank the Center for Information Technology of the University of Groningen for providing access to the Peregrine high-performance computing cluster. We also acknowledge the National Computing Facilities Foundation of The Netherlands Organization for Scientific Research (NWO) for providing computing time. L.B.A. and P.C.T.S. would like to thank the support of the French National Center for Scientific Research (CNRS) and the funding from research collaboration agreements with PharmCADD. S.J.M. received funding from the European Research Council (ERC) through an ERC Advanced grant \u201CCOMP-MICR-CROW-MEM\u201D. S.T. acknowledges the support from the European Commission via a Marie Sk\u0142odowska-Curie Actions individual fellowship (MicroMod-PSII, grant agreement 748895), the Center for Multiscale Modeling in Life Sciences (CMMS), the Alfons und Gertrud Kassel Foundation, and the Dr. Rolf M. Schwiete Foundation. L.M. acknowledges funding by the Institut National de la Sant\u00E9 et de la Recherche M\u00E9dicale (INSERM), CC-IN2P3 (https://cc.in2p3.fr), and the French supercomputing centers CINES and TGCC, supported by Grand Equipement National de Calcul Intensif (GENCI), for computing resources and services (grants number A0120710138, A0140710138). M.N.M. acknowledges Funda\u00E7\u00E3o para a Ci\u00EAncia e a Tecnologia for fellowship CEECIND/04124/2017/CP1428/CT0008. A.B.P and R.A.M. acknowledge Marek Cieplak for sharing the source code of the OV + rCSU contact map in Fortran. P.P. acknowledges FAPESP support (grant 2019/26557-8). A.B.P. acknowledges financial support from the National Science Center, Poland, under grant 2022/45/B/NZ1/02519 and gratefully acknowledges Polish high-performance computing infrastructure PLGrid (HPC Centers: ACK Cyfronet AGH) for providing computer facilities and support within computational grant no. PLG/2023/016519. R.M.-A. thanks, ANID-Chile, for financial support under FONDECYT N. 1200200. Funding Information: This work was granted access to the HPC resources of IDRIS and TGCC under the allocations 2022-A0120713456 (P.C.T.S) and 2023-A0140713456 (P.C.T.S.) made by GENCI. We also acknowledge the support of the Center Blaise Pascal\u2019s IT test platform at ENS de Lyon (Lyon, France) for the computer facilities. The platform operates the SIDUS solution developed by Emmanuel Quemener. We thank the Center for Information Technology of the University of Groningen for providing access to the Peregrine high-performance computing cluster. We also acknowledge the National Computing Facilities Foundation of The Netherlands Organization for Scientific Research (NWO) for providing computing time. L.B.A. and P.C.T.S. would like to thank the support of the French National Center for Scientific Research (CNRS) and the funding from research collaboration agreements with PharmCADD. S.J.M. received funding from the European Research Council (ERC) through an ERC Advanced grant \u201CCOMP-MICR-CROW-MEM\u201D. S.T. acknowledges the support from the European Commission via a Marie Sk\u0142odowska-Curie Actions individual fellowship (MicroMod-PSII, grant agreement 748895), the Center for Multiscale Modeling in Life Sciences (CMMS), the Alfons und Gertrud Kassel Foundation, and the Dr. Rolf M. Schwiete Foundation. L.M. acknowledges funding by the Institut National de la Sant\u00E9 et de la Recherche M\u00E9dicale (INSERM), CC-IN2P3 ( https://cc.in2p3.fr ), and the French supercomputing centers CINES and TGCC, supported by Grand Equipement National de Calcul Intensif (GENCI), for computing resources and services (grants number A0120710138, A0140710138). M.N.M. acknowledges Funda\u00E7\u00E3o para a Ci\u00EAncia e a Tecnologia for fellowship CEECIND/04124/2017/CP1428/CT0008. A.B.P and R.A.M. acknowledge Marek Cieplak for sharing the source code of the OV\u2009+\u2009rCSU contact map in Fortran. P.P. acknowledges FAPESP support (grant 2019/26557-8). A.B.P. acknowledges financial support from the National Science Center, Poland, under grant 2022/45/B/NZ1/02519 and gratefully acknowledges Polish high-performance computing infrastructure PLGrid (HPC Centers: ACK Cyfronet AGH) for providing computer facilities and support within computational grant no. PLG/2023/016519. R.M.-A. thanks, ANID-Chile, for financial support under FONDECYT N. 1200200. Publisher Copyright: © The Author(s) 2025.