@article {2020|2117, title = {Aggregation of disease-related peptides.}, journal = {Prog Mol Biol Transl Sci}, volume = {170}, year = {2020}, month = {2020}, pages = {435-460}, abstract = {

Protein misfolding and aggregation of amyloid proteins is the fundamental cause of more than 20 diseases. Molecular mechanisms of the self-assembly and the formation of the toxic aggregates are still elusive. Computer simulations have been intensively used to study the aggregation of amyloid peptides of various amino acid lengths related to neurodegenerative diseases. We review atomistic and coarse-grained simulations of short amyloid peptides aimed at determining their transient oligomeric structures and the early and late aggregation steps.

}, issn = {1878-0814}, doi = {10.1016/bs.pmbts.2019.12.002}, author = {Phuong Hoang Nguyen and Sterpone, Fabio and Philippe Derreumaux} } @article {2019|2109, title = {Amyloid-β (29{\textendash}42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids}, journal = {The Journal of Physical Chemistry B}, volume = {123}, year = {2019}, pages = {2687{\textendash}2696}, author = {Lu, Yan and Shi, Xiao-Feng and Phuong Hoang Nguyen and Sterpone, Fabio and Salsbury Jr, Freddie R and Philippe Derreumaux} } @article {2018|2113, title = {Amyloid-β/drug interactions from computer simulations and cell-based assays}, journal = {Journal of Alzheimer{\textquoteright}s Disease}, volume = {64}, year = {2018}, pages = {S659{\textendash}S672}, author = {Phuong Hoang Nguyen and Del Castillo-Frias, Maria P and Berthoumieux, Olivia and Faller, Peter and Doig, Andrew J and Philippe Derreumaux} } @article {2018|2086, title = {Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network.}, journal = {Sci Rep}, volume = {8}, year = {2018}, month = {2018 09 10}, pages = {13540}, abstract = {

Given the tight relation between protein structure and function, we present a set of methods to analyze protein topology, implemented in the VLDP program, relying on Laguerre space partitions built from series of molecular dynamics snapshots. The Laguerre partition specifies inter-atomic contacts, formalized in graphs. The deduced properties are the existence and count of water aggregates, possible passage ways and constrictions, the structure, connectivity, stability and depth of the water network. As a test-case, the membrane protein FepA is investigated in its full environment, yielding a more precise description of the protein surface. Inside FepA, the solvent splits into isolated clusters and an intricate network connecting both sides of the lipid bilayer. The network is dynamic, connections set on and off, occasionally substantially relocating traversing paths. Subtle differences are detected between two forms of FepA, ligand-free and complexed with its natural iron carrier, the enterobactin. The complexed form has more constricted and more centered openings in the upper part whereas, in the lower part, constriction is released: two main channels between the plug and barrel lead directly to the periplasm. Reliability, precision and the variety of topological features are the main interest of the method.

}, keywords = {Bacterial Outer Membrane Proteins, Carrier Proteins, Enterobactin, Molecular Dynamics Simulation, Protein Stability, Protein Structure, Secondary, Receptors, Cell Surface, Structure-Activity Relationship, Water}, issn = {2045-2322}, doi = {10.1038/s41598-018-31422-5}, author = {Esque, J{\'e}r{\'e}my and Sansom, Mark S P and Marc Baaden and Oguey, Christophe} } @inbook {2018|2085, title = {Applications to water transport systems: general discussion.}, booktitle = {Faraday Discuss}, volume = {209}, year = {2018}, month = {2018 09 28}, pages = {389-414}, issn = {1364-5498}, doi = {10.1039/c8fd90022a}, author = {Marc Baaden and Barboiu, Mihail and Borthakur, Manash Pratim and Chen, Chun-Long and Coalson, Rob and Davis, Jeffery and Freger, Viatcheslav and Gong, Bing and H{\'e}lix-Nielsen, Claus and Hickey, Robert and Hinds, Bruce and Hirunpinyopas, Wisit and Horner, Andreas and Hou, Jun-Li and Hummer, Gerhard and Iamprasertkun, Pawin and Kazushi, Kinbara and Kumar, Manish and Legrand, Yves-Marie and Lokesh, Mahesh and Mi, Baoxia and Mitra, Sushanta and Murail, Samuel and Noy, Aleksandr and Nunes, Suzana and Pohl, Peter and Song, Qilei and Song, Woochul and T{\"o}rnroth-Horsefield, Susanna and Vashisth, Harish} } @article {2017|2024, title = {Ab Initio Simulations of Water Dynamics in Aqueous TMAO Solutions: Temperature and Concentration Effects}, journal = {J Phys Chem B}, year = {2017}, month = {Dec}, abstract = {

We use ab initio molecular dynamics simulation to study the effect of hydrophobic groups on the dynamics of water molecules in aqueous solutions of trimethylamine N-oxide (TMAO). We show that hydrophobic groups induce a moderate (\<2-fold) slowdown of water reorientation and hydrogen-bond dynamics in dilute solutions, but that this slowdown rapidly increases with solute concentration. In addition, the slowdown factor is found to vary very little with temperature, thus suggesting an entropic origin. All of these results are in quantitative agreement with prior classical molecular dynamics simulations and with the previously suggested excluded-volume model. The hydrophilic TMAO headgroup is found to affect water dynamics more strongly than the hydrophobic moiety, and the magnitude of this slowdown is very sensitive to the strength of the water-solute hydrogen-bond.

}, doi = {10.1021/acs.jpcb.7b09989}, author = {Guillaume Stirnemann and Elise Dubou{\'e}-Dijon and Laage, Damien} } @article {2017|2022, title = {ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences}, journal = {Nucleic Acids Res}, volume = {45}, year = {2017}, pages = {8448-8462}, abstract = {

During DNA recombination and repair, RecA family proteins must promote rapid joining of homologous DNA. Repeated sequences with \>100 base pair lengths occupy more than 1\% of bacterial genomes; however, commitment to strand exchange was believed to occur after testing ~20-30 bp. If that were true, pairings between different copies of long repeated sequences would usually become irreversible. Our experiments reveal that in the presence of ATP hydrolysis even 75 bp sequence-matched strand exchange products remain quite reversible. Experiments also indicate that when ATP hydrolysis is present, flanking heterologous dsDNA regions increase the reversibility of sequence matched strand exchange products with lengths up to ~75 bp. Results of molecular dynamics simulations provide insight into how ATP hydrolysis destabilizes strand exchange products. These results inspired a model that shows how pairings between long repeated sequences could be efficiently rejected even though most homologous pairings form irreversible products.

}, doi = {10.1093/nar/gkx582}, author = {Danilowicz, Claudia and Hermans, Laura and Coljee, Vincent and Chantal Pr{\'e}vost and Prentiss, Mara} } @conference {2016|1606, title = {Alzheimer{\textquoteright}s Disease: Insights into Amyloid Fibril Formation from Lattice Monte Carlo Simulations}, booktitle = {Biophys. J.}, volume = {110}, number = {3, 1}, year = {2016}, note = {60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, FEB 27-MAR 02, 2016}, month = {feb}, pages = {219A}, publisher = {Biophys Soc}, organization = {Biophys Soc}, issn = {0006-3495}, author = {Thanh-Thuy Tran and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2016|2115, title = {Aβ41 Aggregates More Like Aβ40 than Like Aβ42: In Silico and in Vitro Study}, journal = {The Journal of Physical Chemistry B}, volume = {120}, year = {2016}, pages = {7371{\textendash}7379}, author = {Nguyen, Hoang Linh and Thi Minh Thu, Tran and Truong, Phan Minh and Lan, Pham Dang and Man, Viet Hoang and Phuong Hoang Nguyen and Tu, Ly Anh and Chen, Yi-Cheng and Li, Mai Suan} } @article {2015|1716, title = {Ab initio RNA folding}, journal = {Journal of Physics-condensed Matter}, volume = {27}, number = {23}, year = {2015}, month = {jun}, pages = {233102}, doi = {10.1088/0953-8984/27/23/233102}, author = {Cragnolini, Tristan and Philippe Derreumaux and Pasquali, Samuela} } @article {2015|1667, title = {The adaptive biasing force method: everything you always wanted to know but were afraid to ask.}, journal = {J. Phys. Chem. B}, volume = {119}, year = {2015}, month = {jan}, pages = {1129{\textendash}51}, abstract = {

In the host of numerical schemes devised to calculate free energy differences by way of geometric transformations, the adaptive biasing force algorithm has emerged as a promising route to map complex free-energy landscapes. It relies upon the simple concept that as a simulation progresses, a continuously updated biasing force is added to the equations of motion, such that in the long-time limit it yields a Hamiltonian devoid of an average force acting along the transition coordinate of interest. This means that sampling proceeds uniformly on a flat free-energy surface, thus providing reliable free-energy estimates. Much of the appeal of the algorithm to the practitioner is in its physically intuitive underlying ideas and the absence of any requirements for prior knowledge about free-energy landscapes. Since its inception in 2001, the adaptive biasing force scheme has been the subject of considerable attention, from in-depth mathematical analysis of convergence properties to novel developments and extensions. The method has also been successfully applied to many challenging problems in chemistry and biology. In this contribution, the method is presented in a comprehensive, self-contained fashion, discussing with a critical eye its properties, applicability, and inherent limitations, as well as introducing novel extensions. Through free-energy calculations of prototypical molecular systems, many methodological aspects are examined, from stratification strategies to overcoming the so-called hidden barriers in orthogonal space, relevant not only to the adaptive biasing force algorithm but also to other importance-sampling schemes. On the basis of the discussions in this paper, a number of good practices for improving the efficiency and reliability of the computed free-energy differences are proposed.

}, issn = {1520-5207}, doi = {10.1021/jp506633n}, author = {Comer, Jeffrey and Gumbart, James C and J{\'e}r{\^o}me H{\'e}nin and Leli{\`e}vre, Tony and Pohorille, Andrew and Christophe Chipot} } @article {2015|1737, title = {Algebraic Statistics of Poincar{\'e} Recurrences in a DNA Molecule.}, journal = {Phys. Rev. Lett.}, volume = {115}, year = {2015}, month = {oct}, pages = {188104}, abstract = {

The statistics of Poincar{\'e} recurrences is studied for the base-pair breathing dynamics of an all-atom DNA molecule in a realistic aqueous environment with thousands of degrees of freedom. It is found that at least over five decades in time the decay of recurrences is described by an algebraic law with the Poincar{\'e} exponent close to β=1.2. This value is directly related to the correlation decay exponent ν=β-1, which is close to ν\≈0.15 observed in the time resolved Stokes shift experiments. By applying the virial theorem we analyze the chaotic dynamics in polynomial potentials and demonstrate analytically that an exponent β=1.2 is obtained assuming the dominance of dipole-dipole interactions in the relevant DNA dynamics. Molecular dynamics simulations also reveal the presence of strong low frequency noise with the exponent η=1.6. We trace parallels with the chaotic dynamics of symplectic maps with a few degrees of freedom characterized by the Poincar{\'e} exponent β\∼1.5.

}, issn = {1079-7114}, doi = {10.1103/PhysRevLett.115.188104}, author = {Alexey K Mazur and Shepelyansky, D L} } @article {2015|1634, title = {Amyloid beta Protein and Alzheimer{\textquoteright}s Disease: When Computer Simulations Complement Experimental Studies}, journal = {Chem. Rev.}, volume = {115}, number = {9}, year = {2015}, month = {may}, pages = {3518{\textendash}3563}, doi = {10.1021/cr500638n}, author = {Nasica-Labouze, Jessica and Phuong Hoang Nguyen and Fabio Sterpone and Berthoumieu, Olivia and Buchete, Nicolae-Viorel and Cote, Sebastien and De Simone, Alfonso and Doig, Andrew J. and Faller, Peter and Garcia, Angel and Laio, Alessandro and Li, Mai Suan and Melchionna, Simone and Mousseau, Normand and Mu, Yuguang and Paravastu, Anant and Pasquali, Samuela and Rosenman, David J. and Strodel, Birgit and Tarus, Bogdan and Viles, John H. and Zhang, Tong and Wang, Chunyu and Philippe Derreumaux} } @article {2015|1910, title = {Are coarse-grained models apt to detect protein thermal stability? The case of \{OPEP\} force field}, journal = {J. Non-cryst. Solids}, volume = {407}, year = {2015}, note = {7th IDMRCS: Relaxation in Complex Systems}, pages = {494{\textendash}501}, keywords = {Conformational substates network}, doi = {10.1016/j.jnoncrysol.2014.07.005}, url = {http://www.sciencedirect.com/science/article/pii/S0022309314002889}, author = {Maria Kalimeri and Philippe Derreumaux and Fabio Sterpone} } @article {2014|1792, title = {Allosteric regulation of pentameric ligand-gated ion channels: An emerging mechanistic perspective}, journal = {Channels}, volume = {8}, number = {4}, year = {2014}, pages = {350{\textendash}360}, keywords = {Allosteric Regulation, Animals, chemistry/metabolism, Humans, Ion Channel Gating, Ligand-Gated Ion Channels, metabolism, Models, Molecular, Protein Multimerization, Small Molecule Libraries}, author = {Antoine Taly and J{\'e}r{\^o}me H{\'e}nin and Changeux, Jean-Pierre and Cecchini, Marco} } @article {2014|1888, title = {Amyloid oligomer structure characterization from simulations: A general method}, journal = {J. Chem. Phys.}, volume = {140}, number = {9}, year = {2014}, month = {mar}, pages = {094105}, doi = {10.1063/1.4866902}, author = {Phuong Hoang Nguyen and Li, Mai Suan and Philippe Derreumaux} } @article {2014|1931, title = {Assessing the effect of dynamics on the closed-loop protein-folding hypothesis}, journal = {Journal of the Royal Society Interface}, volume = {11}, number = {91}, year = {2014}, pages = {20130935}, doi = {10.1098/rsif.2013.0935}, url = {http://rsif.royalsocietypublishing.org/content/11/91/20130935.abstract}, author = {Chintapalli, Sree V. and Illingworth, Christopher J. R. and Upton, Graham J. G. and S Sacquin-Mora and Reeves, Philip J. and Mohammedali, Hani S. and Reynolds, Christopher A.} } @article {2014|1380, title = {Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-L-tryptophan Inhibitor on Alzheimer{\textquoteright}s A beta 1-42 Dimer in Terms of Aggregation and Toxicity}, journal = {Acs Chem. Neurosci.}, volume = {5}, number = {2}, year = {2014}, month = {feb}, pages = {148{\textendash}159}, author = {Zhang, Tong and Xu, Weixin and Mu, Yuguang and Philippe Derreumaux} } @article {2014|1945, title = {Atomic force microscopy study of DNA flexibility on short length scales: Smooth bending versus kinking}, journal = {Nucleic. Acids. Res.}, volume = {42}, year = {2014}, pages = {14006{\textendash}14012}, author = {Alexey K Mazur and Mounir Maaloum} } @article {2013|1699, title = {Agonist-dependent endocytosis of $\gamma$-aminobutyric acid type A (GABAA) receptors revealed by a $\gamma$2 (R43Q) epilepsy mutation}, journal = {J. Biol. Chem.}, volume = {288}, number = {39}, year = {2013}, pages = {28254{\textendash}28265}, publisher = {American Society for Biochemistry and Molecular Biology}, author = {Chaumont, Severine and Andr{\'e}, Caroline and Perrais, David and Bou{\'e}-Grabot, Eric and Antoine Taly and Garret, Maurice} } @article {2013|1938, title = {Allosteric signaling and dynamics of the clamshell-like NMDA receptor GluN1 N-terminal domain}, journal = {Nature Structural \& Molecular Biology}, volume = {20}, number = {4}, year = {2013}, pages = {477{\textendash}485}, publisher = {Nature Publishing Group}, author = {Zhu, Shujia and Stroebel, David and Yao, C Andrea and Antoine Taly and Paoletti, Pierre} } @inbook {2012|1575, title = {Advances in Human-Protein Interaction - Interactive And Immersive Molecular Simulations}, year = {2012}, publisher = {Intech, Croatia}, organization = {Intech, Croatia}, chapter = {Protein Interaction / Book 2}, author = {A. Tek and B. Laurent and M. Piuzzi and Z. Lu and Marc Baaden and O. Delalande and Matthieu Chavent and Nicolas F{\'e}rey and C. Martin and L. Piccinali and B. Katz and P. Bourdot and Ludovic Autin}, editor = {W. Cai and H. Hong} } @article {2012|1642, title = {$\alpha$7 nicotinic acetylcholine receptors: a therapeutic target in the structure era}, journal = {Curr. Drug Targets}, volume = {13}, number = {5}, year = {2012}, pages = {695{\textendash}706}, publisher = {Bentham Science Publishers}, author = {Antoine Taly and Charon, S{\'e}bastien} } @article {2012|1934, title = {{ATTRACT} and {PTOOLS}: {O}pen source programs for protein-protein docking}, journal = {Methods Mol. Biol.}, volume = {819}, year = {2012}, pages = {221{\textendash}232}, abstract = {

The prediction of the structure of protein-protein complexes based on structures or structural models of isolated partners is of increasing importance for structural biology and bioinformatics. The ATTRACT program can be used to perform systematic docking searches based on docking energy minimization. It is part of the object-oriented PTools library written in Python and C++. The library contains various routines to manipulate protein structures, to prepare and perform docking searches as well as analyzing docking results. It also intended to facilitate further methodological developments in the area of macromolecular docking that can be easily integrated. Here, we describe the application of PTools to perform systematic docking searches and to analyze the results. In addition, the possibility to perform multi-component docking will also be presented.

}, doi = {10.1007/978-1-61779-465-0_15}, author = {Schneider, S. and A Saladin and Fiorucci, S. and Chantal Pr{\'e}vost and Martin Zacharias} } @article {2011|1654, title = {Accounting for large amplitude protein deformation during in silico macromolecular docking}, journal = {Int. J. Mol. Sci.}, volume = {12}, year = {2011}, pages = {1316{\textendash}33}, abstract = {

Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.

}, keywords = {flexibility, macromolecular docking, protein loops and domains}, doi = {10.3390/ijms12021316}, author = {Bastard, Karine and A Saladin and Chantal Pr{\'e}vost} } @article {2011|1891, title = {Assessing the Quality of the OPEP Coarse-Grained Force Field}, journal = {J. Chem. Theory Comput.}, volume = {7}, number = {6}, year = {2011}, month = {jun}, pages = {1928{\textendash}1934}, doi = {10.1021/ct100646f}, author = {Barducci, Alessandro and Bonomi, Massimiliano and Philippe Derreumaux} } @article {2010|1950, title = {Anharmonic torsional stiffness of DNA revealed under small external torques}, journal = {Phys. Rev. Lett.}, volume = {105}, year = {2010}, pages = {018102}, author = {Alexey K Mazur} } @article {2010|1865, title = {An atomistic model for simulations of the general anesthetic isoflurane}, journal = {J. Phys. Chem. B}, volume = {114}, number = {1}, year = {2010}, pages = {604{\textendash}612}, publisher = {Laboratoire d{\textquoteright}Ing{\'e}nierie des Syst{\`e}mes Macromol{\'e}culaires, CNRS, Marseille, France. jhenin@ifr88.cnrs-mrs.fr}, abstract = {An atomistic model of isoflurane is constructed and calibrated to describe its conformational preferences and intermolecular interactions. The model, which is compatible with the CHARMM force field for biomolecules, is based on target quantities including bulk liquid properties, molecular conformations, and local interactions with isolated water molecules. Reference data is obtained from tabulated thermodynamic properties and high-resolution structural information from gas-phase electron diffraction, as well as DFT calculations at the B3LYP level. The model is tested against experimentally known solvation properties in water and oil, and shows quantitative agreement. In particular, isoflurane is faithfully described as lipophilic, yet nonhydrophobic, a combination of properties critical to its pharmacological activity. Intermolecular interactions of the model are further probed through simulations of the binding of isoflurane to a binding site in horse spleen apoferritin (HSAF). The observed binding mode compares well with crystallographic data, and the calculated binding affinities are compatible with experimental results, although both computational and experimental measurements are challenging and provide results with limited precision. The model is expected to be useful for detailed simulations of the elementary molecular processes associated with anesthesia. Full parameters are provided as Supporting Information.}, doi = {10.1021/jp9088035}, author = {J{\'e}r{\^o}me H{\'e}nin and Grace Brannigan and William P Dailey and Roderic G Eckenhoff and Michael L Klein} } @article {2009|1947, title = {Analysis of accordion DNA stretching revealed by the gold cluster ruler}, journal = {Phys. Rev. E}, volume = {80}, year = {2009}, pages = {010901}, author = {Alexey K Mazur} } @article {2008|1808, title = {Anomalous diffusion of ions at the surface of hydrated DNA molecule}, journal = {Europhys. Lett.}, volume = {82}, year = {2008}, pages = {46002}, author = {Alla Oleinikova and Ivan Brovchenko and Aliaksei Krukau and Alexey K Mazur} } @conference {2007|1517, title = {Atomistic modeling of the membrane-embedded synaptic fusion complex: a grand challenge project on the DEISA HPC infrastructure}, booktitle = {ParCo 2007, Parallel Computing: Architectures, Algorithms and Applications}, volume = {38}, year = {2007}, pages = {729{\textendash}736}, publisher = {John von Neumann Institute for Computing, Juelich, Germany.}, organization = {John von Neumann Institute for Computing, Juelich, Germany.}, url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=8468}, author = {E. Krieger and L. Leger and M.P. Durrieu and N. Taib and P. Bond and M. Laguerre and R. Lavery and M.S.P. Sansom and Marc Baaden}, editor = {C.B.G.R. Joubert and F. Peters and T. Lippert and M. Buecker and B. Gibbon and and B. Mohr} } @article {2006|1536, title = {Accounting for loop flexibility during protein-protein docking}, journal = {Proteins}, volume = {62}, number = {4}, year = {2006}, month = {mar}, pages = {956{\textendash}969}, author = {Bastard, K and Chantal Pr{\'e}vost and Martin Zacharias} } @article {2006|1981, title = {Aggregating the amyloid A beta(11-25) peptide into a four-stranded beta-sheet structure}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {65}, number = {4}, year = {2006}, month = {dec}, pages = {877{\textendash}888}, doi = {10.1002/prot.21134}, author = {Boucher, Genevive and Mousseau, Normand and Philippe Derreumaux} } @article {2006|1983, title = {ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {63}, number = {4}, year = {2006}, month = {jun}, pages = {967{\textendash}975}, doi = {10.1002/prot.20938}, author = {Yun, MR and Lavery, R and Mousseau, N and Zakrzewska, K and Philippe Derreumaux} } @article {2004|1867, title = {The antitumor properties of the alpha 3(IV)-(185-203) peptide from the NC1 domain of type IV collagen (tumstatin) are conformation-dependent}, journal = {J. Biol. Chem.}, volume = {279}, number = {3}, year = {2004}, month = {jan}, pages = {2091{\textendash}2100}, doi = {10.1074/jbc.M307736200}, author = {Floquet, N and Pasco, S and Ramont, L and Philippe Derreumaux and Laronze, JY and Nuzillard, JM and Maquart, FX and Alix, AJP and Monboisse, JC} } @article {2002, title = {Analysis of Protein Sequence/Structure Similarity Relationships}, journal = {Biophys. J.}, volume = {83}, year = {2002}, pages = {2781{\textendash}2791}, author = {H. H. Gan and R. A. Perow and S. Roy and J. Ko, M. Wu, J. Huang and S. Yan and A. Nicoletta and J. Vafai, D. Sun and L. Wang and J. E. Noah and S. Pasquali and T. Schlick} } @article {2000|1997, title = {Ab initio polypeptide structure prediction}, journal = {Theor. Chem. Acc.}, volume = {104}, number = {1}, year = {2000}, month = {may}, pages = {1{\textendash}6}, doi = {10.1007/s002149900095}, author = {Philippe Derreumaux} } @article {1999|1803, title = {Ab initio prediction of polypeptide structure from its sequence}, journal = {Comput. Phys. Commun.}, volume = {122}, number = {Sp. Iss. SI}, year = {1999}, month = {sep}, pages = {139{\textendash}140}, doi = {10.1016/S0010-4655(99)00299-4}, author = {Philippe Derreumaux} } @article {1998|1835, title = {Accurate DNA dynamics without accurate long range electrostatics}, journal = {J. Am. Chem. Soc.}, volume = {120}, number = {42}, year = {1998}, pages = {10928{\textendash}10937}, author = {Alexey K Mazur} } @article {1989|1785, title = {Allosteric formulation of thermal transitions in macromolecules, including effects of ligand binding and oligomerization}, journal = {Biopolymers}, volume = {28}, number = {10}, year = {1989}, month = {oct}, pages = {1705{\textendash}1729}, author = {Robert, C H and Colosimo, A and Gill, S J} } @article {1988|1597, title = {Analysis and parameter resolution in highly cooperative systems}, journal = {Biophys. Chem.}, volume = {30}, number = {2}, year = {1988}, month = {jun}, pages = {133{\textendash}141}, author = {Gill, S J and Connelly, P R and Di Cera, E and Charles H. Robert} } @inbook {1988, title = {Analysis of allosteric systems}, booktitle = {Biochemical Thermodynamics}, year = {1988}, publisher = {Elsevier}, organization = {Elsevier}, edition = {2nd}, address = {Holland}, author = {Gill, S. J. and Robert, C. H. and Wyman, J.} } @article {1987|1777, title = {Allosteric interpretation of the oxygen-binding reaction of human hemoglobin tetramers}, journal = {Biochemistry}, volume = {26}, number = {13}, year = {1987}, month = {jun}, pages = {4003{\textendash}4008}, author = {Di Cera, E and Robert, C H and Gill, S J} } @article {1986, title = {Active sites of the endo-beta-1,3-glucanases from Spisula sacchalinensis and Chlyamys albidys}, journal = {Bioorg. Chem.}, volume = {12}, year = {1986}, pages = {1478{\textendash}1483}, author = {N. I. Nazarova and Alexey K Mazur and L. A. Elyakova} } @article {1986|1781, title = {Analysis of zeros of binding polynomials for tetrameric hemoglobins}, journal = {Biophys. Chem.}, volume = {24}, number = {3}, year = {1986}, month = {aug}, pages = {295{\textendash}309}, author = {Connelly, P R and Charles H. Robert and Briggs, W E and Gill, S J} }