@article {2021|2149, title = {Fast and Accurate Multidimensional Free Energy Integration.}, journal = {J Chem Theory Comput}, volume = {17}, year = {2021}, month = {2021 Nov 09}, pages = {6789-6798}, abstract = {

Enhanced sampling and free energy calculation algorithms of the thermodynamic integration family (such as the adaptive biasing force (ABF) method) are not based on the direct computation of a free energy surface but rather of its gradient. Integrating the free energy surface is nontrivial in dimensions higher than one. Here, the author introduces a flexible, portable implementation of a Poisson equation formalism to integrate free energy surfaces from estimated gradients in dimensions 2 and 3 using any combination of periodic and nonperiodic (Neumann) boundary conditions. The algorithm is implemented in portable C++ and provided as a standalone tool that can be used to integrate multidimensional gradient fields estimated on a grid using any algorithm, such as umbrella integration as a post-treatment of umbrella sampling simulations. It is also included in the implementation of ABF (and its extended-system variant eABF) in the Collective Variables Module, enabling the seamless computation of multidimensional free energy surfaces within ABF and eABF simulations. A Python-based analysis toolchain is provided to easily plot and analyze multidimensional ABF simulation results, including metrics to assess their convergence. The Poisson integration algorithm can also be used to perform Helmholtz decomposition of noisy gradient estimates on the fly, resulting in an efficient implementation of the projected ABF (pABF) method proposed by Leli{\'e}vre and co-workers. In numerical tests, pABF is found to lead to faster convergence with respect to ABF in simple cases of low intrinsic dimension but seems detrimental to convergence in a more realistic case involving degenerate coordinates and hidden barriers due to slower exploration. This suggests that variance reduction schemes do not always yield convergence improvements when applied to enhanced sampling methods.

}, issn = {1549-9626}, doi = {10.1021/acs.jctc.1c00593}, author = {J{\'e}r{\^o}me H{\'e}nin} } @article {2018|2132, title = {The force-dependent mechanism of DnaK-mediated mechanical folding}, journal = {Sci Adv}, volume = {4}, year = {2018}, month = {Feb}, pages = {eaaq0243}, abstract = {

It is well established that chaperones modulate the protein folding free-energy landscape. However, the molecular determinants underlying chaperone-mediated mechanical folding remain largely elusive, primarily because the force-extended unfolded conformation fundamentally differs from that characterized in biochemistry experiments. We use single-molecule force-clamp spectroscopy, combined with molecular dynamics simulations, to study the effect that the Hsp70 system has on the mechanical folding of three mechanically stiff model proteins. Our results demonstrate that, when working independently, DnaJ (Hsp40) and DnaK (Hsp70) work as holdases, blocking refolding by binding to distinct substrate conformations. Whereas DnaK binds to molten globule-like forms, DnaJ recognizes a cryptic sequence in the extended state in an unanticipated force-dependent manner. By contrast, the synergetic coupling of the Hsp70 system exhibits a marked foldase behavior. Our results offer unprecedented molecular and kinetic insights into the mechanisms by which mechanical force finely regulates chaperone binding, directly affecting protein elasticity.

}, doi = {10.1126/sciadv.aaq0243}, author = {Perales-Calvo, Judit and Giganti, David and Guillaume Stirnemann and Garcia-Manyes, Sergi} } @article {2018|2136, title = {Forcing the reversibility of a mechanochemical reaction}, journal = {Nat Commun}, volume = {9}, year = {2018}, month = {08}, pages = {3155}, abstract = {

Mechanical force modifies the free-energy surface of chemical reactions, often enabling thermodynamically unfavoured reaction pathways. Most of our molecular understanding of force-induced reactivity is restricted to the irreversible homolytic scission of covalent bonds and ring-opening in polymer mechanophores. Whether mechanical force can by-pass thermodynamically locked reactivity in heterolytic bimolecular reactions and how this impacts the reaction reversibility remains poorly understood. Using single-molecule force-clamp spectroscopy, here we show that mechanical force promotes the thermodynamically disfavored SN2 cleavage of an individual protein disulfide bond by poor nucleophilic organic thiols. Upon force removal, the transition from the resulting high-energy unstable mixed disulfide product back to the initial, low-energy disulfide bond reactant becomes suddenly spontaneous, rendering the reaction fully reversible. By rationally varying the nucleophilicity of a series of small thiols, we demonstrate how force-regulated chemical kinetics can be finely coupled with thermodynamics to predict and modulate the reversibility of bimolecular mechanochemical reactions.

}, doi = {10.1038/s41467-018-05115-6}, author = {Beedle, Amy E M and Mora, Marc and Davis, Colin T and Snijders, Ambrosius P and Guillaume Stirnemann and Garcia-Manyes, Sergi} } @article {2018|2088, title = {From Virtual Reality to Immersive Analytics in Bioinformatics.}, journal = {J Integr Bioinform}, volume = {15}, year = {2018}, month = {2018 Jul 09}, abstract = {

Bioinformatics-related research produces huge heterogeneous amounts of data. This wealth of information includes data describing metabolic mechanisms and pathways, proteomics, transcriptomics, and metabolomics. Often, the visualization and exploration of related structural - usually molecular - data plays an important role in the aforementioned contexts. For decades, virtual reality (VR)-related technologies were developed and applied to Bioinformatics problems. Often, these approaches provide \"just\" visual support of the analysis, e.g. in the case of exploring and interacting with a protein on a 3D monitor and compatible interaction hardware. Moreover, in the past these approaches were limited to cost-intensive professional visualization facilities. The advent of new affordable, and often mobile technologies, provides high potential for using similar approaches on a regular basis for daily research. Visual Analytics is successfully being used for several years to analyze complex and heterogeneous datasets. Immersive Analytics combines these approaches now with new immersive and interactive technologies. This publication provides a short overview of related technologies, their history and Bioinformatics-related approaches. Six new applications on the path from VR to Immersive Analytics are being introduced and discussed.

}, keywords = {Computer Graphics, Imaging, Three-Dimensional, Molecular Conformation, Proteins, Software, User-Computer Interface, Virtual Reality}, issn = {1613-4516}, doi = {10.1515/jib-2018-0043}, author = {Sommer, Bj{\"o}rn and Marc Baaden and Krone, Michael and Woods, Andrew} } @article {2017|2041, title = {Fast coarse-grained model for RNA titration.}, journal = {J Chem Phys}, volume = {146}, year = {2017}, month = {2017 Jan 21}, pages = {035101}, abstract = {

A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-H{\"u}ckel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKshifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.

}, keywords = {Azotobacter vinelandii, Introns, Models, Chemical, Molecular Dynamics Simulation, Monte Carlo Method, Protein Structure, Secondary, Protons, RNA, RNA, Catalytic, Titrimetry}, issn = {1089-7690}, doi = {10.1063/1.4972986}, author = {Barroso da Silva, Fernando Luis and Philippe Derreumaux and Pasquali, Samuela} } @article {2015|1833, title = {{F}old and flexibility: what can proteins{\textquoteright} mechanical properties tell us about their folding nucleus?}, journal = {J. R. Soc. Interface}, volume = {12}, number = {112}, year = {2015}, month = {nov}, author = {S Sacquin-Mora} } @article {2015|1713, title = {Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering}, journal = {J. Phys. Chem. B}, volume = {119}, number = {23}, year = {2015}, month = {jun}, pages = {6941{\textendash}6951}, author = {Zhang, Tong and Phuong Hoang Nguyen and Nasica-Labouze, Jessica and Mu, Yuguang and Philippe Derreumaux} } @article {2014|1927, title = {Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the A beta 1-28 Monomer}, journal = {J. Phys. Chem. B}, volume = {118}, number = {2}, year = {2014}, month = {jan}, pages = {501{\textendash}510}, doi = {10.1021/jp4115404}, author = {Phuong Hoang Nguyen and Tarus, Bogdan and Philippe Derreumaux} } @inbook {2014|1720, title = {Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins}, booktitle = {Membrane Proteins Production for Structural Analysis}, year = {2014}, pages = {347{\textendash}392}, publisher = {Springer New York}, organization = {Springer New York}, author = {J{\'e}r{\^o}me H{\'e}nin and Marc Baaden and Antoine Taly} } @article {2013|1525, title = {{F}ormation of raft-like assemblies within clusters of influenza hemagglutinin observed by {M}{D} simulations}, journal = {Plos Comput. Biol.}, volume = {9}, number = {4}, year = {2013}, month = {apr}, pages = {e1003034}, author = {Parton, D. L. and Tek, A. and Marc Baaden and Sansom, M. S.} } @article {2012|1932, title = {Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches}, journal = {Journal of the Royal Society Interface}, volume = {9}, number = {66}, year = {2012}, month = {jan}, pages = {20{\textendash}33}, doi = {10.1098/rsif.2011.0584}, author = {Pierre Tuffery and Philippe Derreumaux} } @article {2011|2014, title = {{F}rom toxins targeting ligand gated ion channels to therapeutic molecules}, journal = {Toxins (basel)}, volume = {3}, number = {3}, year = {2011}, month = {mar}, pages = {260{\textendash}293}, publisher = {Molecular Diversity Preservation International}, author = {Nasiripourdori, A. and Taly, V. and Grutter, T. and Antoine Taly} } @article {2011|1446, title = {{F}rontier residues lining globin internal cavities present specific mechanical properties}, journal = {J. Am. Chem. Soc.}, volume = {133}, year = {2011}, month = {jun}, pages = {8753{\textendash}8761}, author = {Bocahut, A. and Bernad, S. and Sebban, P. and S Sacquin-Mora} } @article {2011|1848, title = {Free energy profiles along consensus normal modes provide insight into {HIV}-1 protease flap opening}, journal = {J. Chem. Theor. Comput.}, volume = {7}, year = {2011}, pages = {2348{\textendash}52}, author = {Paulo R. Batista and Gaurav Pandey and Paulo M. Bisch and Paulo G. Pascutti and David Perahia and Charles H. Robert} } @conference {2011, title = {FvNano: A Virtual Laboratory to Manipulate Molecular Systems}, booktitle = {1st IEEE symposium on biological data visualization, Providence, RI @ ieee visweek, 2011, N$\#$ 136}, year = {2011}, url = {http://www.biovis.net/materials/abstracts/BioVispaper136.pdf}, author = {Matthieu Chavent and Marc Piuzzi and Alex Tek and Marc Baaden} } @article {2010|1901, title = {A Fast Method for Large-Scale De Novo Peptide and Miniprotein Structure Prediction}, journal = {J. Comput. Chem.}, volume = {31}, number = {4}, year = {2010}, month = {mar}, pages = {726{\textendash}738}, doi = {10.1002/jcc.21365}, author = {Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery} } @article {2010|1613, title = {Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress}, journal = {Biophys. J.}, volume = {99}, number = {10}, year = {2010}, pages = {3412{\textendash}3419}, doi = {10.1016/j.bpj.2010.09.026}, author = {S Sacquin-Mora and Delalande, O. and Marc Baaden} } @article {2009|1436, title = {A fast method for large-scale De Novo peptide and miniprotein structure prediction.}, journal = {J. Comput. Chem.}, year = {2009}, month = {jun}, doi = {10.1002/jcc.21365}, author = {Julien Maupetit and Philippe Derreumaux and Pierre Tuffery} } @article {2009|1486, title = {Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis}, journal = {J. Phys. Chem. B}, volume = {113}, number = {52}, year = {2009}, month = {dec}, pages = {16660{\textendash}16668}, author = {Riccardi, Laura and Phuong Hoang Nguyen and Stock, Gerhard} } @article {2008|1999, title = {{F}unctional organization and conformational dynamics of the nicotinic receptor: a plausible structural interpretation of myasthenic mutations}, journal = {Ann. N. Y. Acad. Sci.}, volume = {1132}, number = {1}, year = {2008}, pages = {42{\textendash}52}, publisher = {Wiley Online Library}, author = {Antoine Taly and Jean-Pierre Changeux} } @article {2008|1451, title = {Fluctuation-induced interactions between dielectrics}, journal = {J. Chem. Phys.}, volume = {129}, year = {2008}, pages = {014703}, author = {S. Pasquali and A.C. Maggs} } @conference {2008|1544, title = {Free energy surface of Abeta(16-22) complexed by N-methylated Abeta16-22 inhibitors}, booktitle = {Publication Series of the John von Neumann Institute for Computing NIC Series}, volume = {40}, year = {2008}, pages = {177{\textendash}179}, author = {Y Chebaro and Philippe Derreumaux} } @conference {2008|1557, title = {From Interactive to Immersive Molecular Dynamics}, booktitle = {Workshop on Virtual Reality Interaction and Physical Simulation (VRIPHYS 08 - Eurographics)}, year = {2008}, month = {nov}, pages = {89{\textendash}96}, address = {Grenoble - France}, author = {Nicolas F{\'e}rey and O. Delalande and G. Grasseau and Marc Baaden}, editor = {F. Faure and M. Teschner} } @inbook {2007|1774, title = {{F}lexible macromolecular docking: {A}n overview of recent progress}, volume = {Recent Research Adv. in Structural BioInformatics}, year = {2007}, pages = {249{\textendash}274}, publisher = {Research Signpost}, organization = {Research Signpost}, chapter = {10}, author = {K. Bastard and Chantal Pr{\'e}vost}, editor = {A. G. De Brevern} } @article {2005|1879, title = {Following the aggregation of amyloid-forming peptides by computer simulations}, journal = {J. Chem. Phys.}, volume = {122}, number = {17}, year = {2005}, month = {may}, pages = {174904}, doi = {10.1063/1.1886725}, author = {Melquiond, A and Boucher, G and Mousseau, N and Philippe Derreumaux} } @conference {2005, title = {Following the aggregation of amyloid-forming peptides by computer simulations.}, booktitle = {Abstracts of Papers of the American Chemical Society}, volume = {229}, number = {Part 2}, year = {2005}, pages = {U735}, author = {Philippe Derreumaux} } @article {2005|1538, title = {Free energy landscape and folding mechanism of a beta-hairpin in explicit water: A replica exchange molecular dynamics study}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {61}, number = {4}, year = {2005}, month = {dec}, pages = {795{\textendash}808}, author = {Phuong Hoang Nguyen and Stock, G and Mittag, E and Hu, CK and Li, MS} } @article {2003|1706, title = {Fluid phase transitions at chemically heterogeneous, nonplanar solid substrates: Surface versus confinement effects}, journal = {J. Chem. Phys.}, volume = {118}, number = {3}, year = {2003}, month = {jan}, pages = {1453{\textendash}1465}, doi = {10.1063/1.1529683}, author = {S Sacquin-Mora and Schoen, M. and Fuchs, A. H.} } @mastersthesis {2003|1561, title = {Fluide nanoconfines dans des systemes de basse symetrie : Simulations et Theorie}, year = {2003}, school = {Universit{\'e} Paris XI, Orsay}, type = {phd}, author = {S Sacquin-Mora} } @article {2002|1726, title = {Fluids confined by nanopatterned substrates of low symmetry}, journal = {Mol. Phys.}, volume = {100}, number = {18}, year = {2002}, month = {sep}, pages = {2971{\textendash}2982}, doi = {10.1080/00268970210121632}, author = {S Sacquin-Mora and Schoen, M. and Fuchs, A. H.} } @article {1999|1873, title = {From polypeptide sequences to structures using Monte Carlo simulations and an optimized potential}, journal = {J. Chem. Phys.}, volume = {111}, number = {5}, year = {1999}, month = {aug}, pages = {2301{\textendash}2310}, doi = {10.1063/1.479501}, author = {Philippe Derreumaux} } @article {1998|1872, title = {Finding the low-energy forms of avian pancreatic polypeptide with the diffusion-process-controlled Monte Carlo method}, journal = {J. Chem. Phys.}, volume = {109}, number = {4}, year = {1998}, month = {jul}, pages = {1567{\textendash}1574}, doi = {10.1063/1.476708}, author = {Philippe Derreumaux} } @article {1998|1530, title = {Folding and Aggregation of Designed Protein Chains}, journal = {Proc. Natl. Acad. Sci. Usa}, volume = {95}, year = {1998}, pages = {12930{\textendash}1293}, author = {R.A. Broglia and G. Tiana and S. Pasquali and H. E. Roman and E. Vigezzi} } @article {1997|1870, title = {Folding a 20 amino acid alpha beta peptide with the diffusion process-controlled Monte Carlo method}, journal = {J. Chem. Phys.}, volume = {107}, number = {6}, year = {1997}, month = {aug}, pages = {1941{\textendash}1947}, doi = {10.1063/1.474546}, author = {Philippe Derreumaux} } @article {1996|1666, title = {Finding and visualizing nucleic acid base stacking}, journal = {J Mol Graph}, volume = {14}, number = {1}, year = {1996}, month = {feb}, pages = {6{\textendash}11}, author = {Gabb, H A and Sanghani, S R and Charles H. Robert and Chantal Pr{\'e}vost} } @article {1994|1992, title = {FORCE-FIELD AND VIBRATIONAL-SPECTRA OF OLIGOSACCHARIDES WITH DIFFERENT GLYCOSIDIC LINKAGES .1. TREHALOSE DIHYDRATE, SOPHOROSE MONOHYDRATE AND LAMINARIBIOSE}, journal = {Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy}, volume = {50}, number = {1}, year = {1994}, month = {jan}, pages = {87{\textendash}104}, doi = {10.1016/0584-8539(94)80117-7}, author = {Dauchez, M and Philippe Derreumaux and LAGANT, P and VERGOTEN, G and SEKKAL, M and LEGRAND, P} } @article {1994|1993, title = {FORCE-FIELD AND VIBRATIONAL-SPECTRA OF OLIGOSACCHARIDES WITH DIFFERENT GLYCOSIDIC LINKAGES .2. MALTOSE MONOHYDRATE, CELLOBIOSE AND GENTIOBIOSE}, journal = {Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy}, volume = {50}, number = {1}, year = {1994}, month = {jan}, pages = {105{\textendash}118}, doi = {10.1016/0584-8539(94)80118-5}, author = {Dauchez, M and LAGANT, P and Philippe Derreumaux and VERGOTEN, G and SEKKAL, M and SOMBRET, B} }