Sergei Grudinin

Contact Information

Address: Nano-D, Inria Grenoble, Minatec Campus 17 rue des Martyrs, 38054 Grenoble, France

Telephone: +33 4 38 78 16 91

Email: Sergei.Grudinin@inria.fr

Coordinator of the PPI-3D associate team between Nano-D Inria, France, and  Dima Kozakov’s Lab at Stony Brook University, USA. The goal of this team is to speed up docking approaches to tackle genome-scale problems, and utilize additional information on interactions, sequences, and structures that is available for virtually any protein.

Previously coordinated the PEPSI project. PEPSI (Polynomial Expansions of Protein Structures and Interactions) was a 5-years project, supported by the ANR (French National Agency for Research) in the program Modèles Numériques (MN). The project started on the 01/11/2011. Its main goal was to develop novel algorithmic techniques for structural bioinformatics and apply these to current structural biology research projects. The project partners were David W. Ritchie from Inria Nancy and Valentin Gordeliy from IBS Grenoble.

Short Bio

Sergei Grudinin is a research associate (CR) scientist in the NANO-D group at the INRIA Grenoble – Rhone-Alpes Research Center. He graduated from MIPT in 2002, and did his Ph.D at the research centre of Jülich, Germany.

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Software packages

These are listed here, team.inria.fr/nano-d/software/

Projects

Macromolecular flexibility:

  • Non-linear normal mode analysis.
  • Dimensionality reduction of motion manifolds.

Small-angle scattering:

  • Fast modeling of SAXS profiles.
  • SAXS-assisted structure optimisation.

Protein-Protein and Protein-Ligand Interactions:

  • Development of knowledge-based potentials.
  • Protein docking.

Fast electrostatics:

  • Development of fast multipole algorithms.

Solvation:

  • Solvation effects based on Boundary Element Method.
  • Generalized Born Model.

Symmetry:

  • Geometry optimization and modelling of systems with any type of symmetry.
  • Symmetry-assited docking.
  • Fast electrostatics with symmetry.

Multiscale modelling:

  • Adaptive algorithms for the Molecular Dynamics and minimization.
  • Adaptive fast electrostatics solvers.

Recent Publications

Publications HAL de sergei grudinin

2017

Journal articles

titre
Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization
auteur
Maria Kadukova, Sergei Grudinin
article
Journal of Computer-Aided Molecular Design, Springer Verlag, 2017, 31 (10), pp.943-958. 〈10.1007/s10822-017-0068-8〉
DOI
DOI : 10.1007/s10822-017-0068-8
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01591154/file/2017-Kadukova-Convex-PL%3A%20a%20novel%20knowledge-based%20potential%20for%20protein-ligand%20interactions%20deduced%20from%20structural%20databases%20using%20convex%20optimization.pdf BibTex
titre
Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2
auteur
Maria Kadukova, Sergei Grudinin
article
Journal of Computer-Aided Molecular Design, Springer Verlag, 2017, 〈10.1007/s10822-017-0062-1〉
DOI
DOI : 10.1007/s10822-017-0062-1
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01591157/file/2017-Kadukova-Docking%20of%20small%20molecules%20to%20farnesoid%20X%20receptors%20using%20AutoDock%20Vina%20with%20the%20Convex-PL%20potential%3A%20lessons%20learned%20from%20D3R%20Grand%20Challenge%202.pdf BibTex
titre
A novel fast Fourier transform accelerated off-grid exhaustive search method for cryo-electron microscopy fitting
auteur
Alexandre Hoffmann, Valérie Perrier, Sergei Grudinin
article
Journal of Applied Crystallography, International Union of Crystallography, 2017, 50 (4), pp.1036-1047. 〈10.1107/S1600576717008172〉
DOI
DOI : 10.1107/S1600576717008172
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01553293/file/2017-Hoffmann-preprint-A%20novel%20fast%20Fourier%20transform%20accelerated%20off-grid%20exhaustive%20search%20method%20for%20cryo-electron%20microscopy%20fitting.pdf BibTex
titre
Mechanism of transmembrane signaling by sensor histidine kinases
auteur
Ivan Yu. Gushchin, Igor Melkinov, Vitaly Polovinkin, Andrii Ishchenko, Anastasia Yuzhakova, Pavel Buslaev, Gleb Bourenkov, Sergei Grudinin, Ekaterina Round, Taras Balandin, Valentin Borshchevskiy, Dieter Willbold, Gordon Leonard, Georg Büldt, Alexander Popov, Valentin I. Gordeliy
article
Science, American Association for the Advancement of Science, 2017, 356 (6342), pp.eaah6345. 〈10.1126/science.aah6345〉
DOI
DOI : 10.1126/science.aah6345
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01526454/file/NarQ-Author-Version.pdf BibTex
titre
Pepsi-SAXS : an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles
auteur
Sergei Grudinin, Maria Garkavenko, Andrei Kazennov
article
Acta Crystallographica Section D: Biological Crystallography, International Union of Crystallography, 2017, D73, pp.449 – 464. 〈10.1107/S2059798317005745〉
DOI
DOI : 10.1107/S2059798317005745
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01516719/file/2017-Grudinin-Pepsi-SAXS-an%20adaptive%20method%20for%20rapid%20and%20accurate%20computation%20of%20small-angle%20X-ray%20scattering%20profiles-reprint.pdf BibTex
titre
NOLB: Nonlinear Rigid Block Normal Mode Analysis Method
auteur
Alexandre Hoffmann, Sergei Grudinin
article
Journal of Chemical Theory and Computation, American Chemical Society, 2017, 13 (5), pp.2123-2134. 〈10.1021/acs.jctc.7b00197〉
DOI
DOI : 10.1021/acs.jctc.7b00197
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01505843/file/NOLB-Author-Version.pdf BibTex
titre
Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models
auteur
Marwa El Houasli, Bernard Maigret, Marie-Dominique Devignes, Anisah Ghoorah, Sergei Grudinin, David Ritchie
article
Proteins: Structure, Function, and Genetics, Wiley, 2017, Special Issue: Sixth Meeting on the Critical Assessment of Predicted Interactions 85 (3), pp.463-469. 〈10.1002/prot.25182〉
DOI
DOI : 10.1002/prot.25182
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01388654/file/marwa_proteins.pdf BibTex
titre
New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex
auteur
Andrii Ishchenko, Ekaterina Round, Valentin Borshchevskiy, Sergei Grudinin, Ivan Yu. Gushchin, Johann Klare, Alina Remeeva, Vitaly Polovinkin, Petr Utrobin, Taras Balandin, Martin Engelhard, Georg Büldt, Valentin I. Gordeliy
article
Scientific Reports, Nature Publishing Group, 2017, 7, pp.41811. 〈10.1038/srep41811〉
DOI
DOI : 10.1038/srep41811
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01458744/file/srep41811.pdf BibTex

Preprints, Working Papers, …

titre
User Guide for AnAnaS : Analytical Analyzer of Symmetries
auteur
Guillaume Pagès, Sergei Grudinin
article
2017
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01644987/file/AnAnaS-Manual.pdf BibTex
titre
User Guide for NOLB : Non-Linear Normal Mode Analysis
auteur
Sergei Grudinin
article
2017
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01565129/file/UserGuide.pdf BibTex

2016

Journal articles

titre
Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment
auteur
Marc F. Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen-You Huang, Dina Schneidman-Duhovy, Andrej Sali, Joan Segura, Narcis Fernandez-Fuentes, Shruthi Viswanath, Ron Elber, Sergei Grudinin, Petr Popov, Emilie Neveu, Hasup Lee, Minkyung Baek, Sangwoo Park, Lim Heo, Gyu Rie Lee, Chaok Seok, Sanbo Qin, Huan-Xiang Zhou, David W. Ritchie, Bernard Maigret, Marie-Dominique Devignes, Anisah Ghoorah, Mieczyslaw Torchala, Raphaël Chaleil, Paul A Bates, Efrat Ben-Zeev, Miriam Eisenstein, Surendra Negi S., Thom Vreven, Brian G Pierce, Tyler Borrman, Jinchao Yu, Francoise Ochsenbein, Zhiping Weng, Raphaël Guerois, Anna Vangone, João Rodrigues, Gydo Van Zundert, Mehdi Nellen, Li Xue, Ezgi Karaca, Adrien S. J. Melquiond, Koen Visscher, Panagiotis L Kastritis, Alexandre Bonvin, Xianjin Xu, Liming Qiu, Chengfei Yan, Jilong Li, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Yang Sheng, Lenna Peterson, Hyung-Rae Kim, Amit Roy, Xusi Han, Juan Esquivel-Rodríguez, Daisuke Kihara, Xiaofeng Yu, Neil J. Bruce, Jonathan C. Fuller, Rebbecca Wade, Ivan Anishchenko, Petras Kundrotas, Ilya Vakser, Kenichiro Imai, Kazunori Yamada, Toshiyuki Oda, Tsukasa Nakamura, Kentaro Tomii, Chiara Pallara, Miguel Romero-Durana, Brian Jiménez-García, Iain H Moal, Juan Fernández-Recio, Jong Young Joung, Jong Yun Kim, Keehyoung Joo, Jooyoung Lee, Dima Kozakov, Sandor Vajda, Scott Mottarella, David Hall, Dmitri Beglov, Artem Mamonov, Bing Xia, Tanggis Bohnuud, Carlos Del Carpio, Eichiro Ichiishi, Nicholas Marze, Daisuke Kuroda, Shourya Burman, Jeffrey J Gray, Edrisse Chermak, Luigi Cavallo, Romina Oliva, Andrey Tovchigrechko, Shoshana J Wodak
article
Proteins – Structure, Function and Bioinformatics, Wiley, 2016, Special Issue: Eleventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, 84 (S1), pp.323-348 〈10.1002/prot.25007〉
DOI
DOI : 10.1002/prot.25007
Accès au bibtex
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titre
Predicting binding poses and affinities for protein-ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation
auteur
Sergei Grudinin, Maria Kadukova, Andreas Eisenbarth, Simon Marillet, Frédéric Cazals
article
Journal of Computer-Aided Molecular Design, Springer Verlag, 2016, 30 (9), pp.791-804. 〈10.1007/s10822-016-9976-2〉
DOI
DOI : 10.1007/s10822-016-9976-2
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01377738/file/2016-Grudinin-Predicting%20binding%20poses%20and%20affinities%20for%20protein%20-%20ligand%20complexes%20in%20the%202015%20D3R%20Grand%20Challenge%20using%20a%20physical%20model%20with%20a%20statistical%20parameter%20estimation-post-print.pdf BibTex
titre
PEPSI-Dock: a detailed data-driven protein–protein interaction potential accelerated by polar Fourier correlation
auteur
Emilie Neveu, David Ritchie, Petr Popov, Sergei Grudinin
article
Bioinformatics, Oxford University Press (OUP), 2016, 32 (7), pp.i693-i701. 〈10.1093/bioinformatics/btw443〉
DOI
DOI : 10.1093/bioinformatics/btw443
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01358645/file/Bioinformatics-2016-Neveu-i693-701.pdf BibTex
titre
Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates
auteur
Maria Kadukova, Sergei Grudinin
article
Journal of Chemical Information and Modeling, American Chemical Society, 2016, 56 (8), pp.1410-1419. 〈http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00512〉. 〈10.1021/acs.jcim.5b00512〉
DOI
DOI : 10.1021/acs.jcim.5b00512
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01381010/file/Knodle-AuthorVersion.pdf BibTex
titre
Predicting Binding Poses and Affinities in the CSAR 2013―2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential
auteur
Sergei Grudinin, Petr Popov, Emilie Neveu, Georgy Cheremovskiy
article
Journal of Chemical Information and Modeling, American Chemical Society, 2016, 56 (6), pp.1053-1062. 〈10.1021/acs.jcim.5b00339〉
DOI
DOI : 10.1021/acs.jcim.5b00339
Accès au bibtex
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titre
Principal component analysis of lipid molecule conformational changes in molecular dynamics simulations
auteur
Pavel Buslaev, Valentin I. Gordeliy, Sergei Grudinin, Ivan Yu. Gushchin
article
Journal of Chemical Theory and Computation, American Chemical Society, 2016, 12 (3), pp.1019-1028. 〈10.1021/acs.jctc.5b01106〉
DOI
DOI : 10.1021/acs.jctc.5b01106
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titre
Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry
auteur
David W. Ritchie, Sergei Grudinin
article
Journal of Applied Crystallography, International Union of Crystallography, 2016, 49 (1), pp.158-167. 〈10.1107/S1600576715022931〉
DOI
DOI : 10.1107/S1600576715022931
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01261402/file/ritchie_grudinin_jac_2016.pdf BibTex

Conference papers

titre
Inverse Protein Folding Problem via Quadratic Programming
auteur
Andrii Riazanov, Mikhail Karasikov, Sergei Grudinin
article
Information Technology and Systems 2016, Sep 2016, Repino, St. Petersburg, Russia. pp.561-568, 〈http://itas2016.iitp.ru/en/〉
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01419374/file/Riazanov2016InverseProteinFoldingProblem.pdf BibTex
titre
Quadratic Programming Approach to Fit Protein Complexes into Electron Density Maps
auteur
Roman Pogodin, Alexander Katrutsa, Sergei Grudinin
article
Information Technology and Systems 2016, Sep 2016, Repino, St. Petersburg, Russia. pp.576-582, 2016
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01419380/file/itas.pdf BibTex

2015

Journal articles

titre
Knowledge of Native Protein–Protein Interfaces Is Sufficient To Construct Predictive Models for the Selection of Binding Candidates
auteur
Petr Popov, Sergei Grudinin
article
Journal of Chemical Information and Modeling, American Chemical Society, 2015, 55 (10), pp.2242-2255. 〈10.1021/acs.jcim.5b00372〉
DOI
DOI : 10.1021/acs.jcim.5b00372
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2014

Journal articles

titre
Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges
auteur
Irina Kufareva, Vsevolod Katritch, Sergei Grudinin, Raymond C Stevens, Ruben Abagyan
article
Structure, 2014, 22 (8), pp.1120-1139. 〈10.1016/j.str.2014.06.012〉
DOI
DOI : 10.1016/j.str.2014.06.012
Accès au bibtex
BibTex
titre
HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions
auteur
Georgy Derevyanko, Sergei Grudinin
article
Acta Crystallographica Section D: Biological Crystallography, International Union of Crystallography, 2014, 70 (8), pp.2069-2084. 〈10.1107/S1399004714011493〉
DOI
DOI : 10.1107/S1399004714011493
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01078550/file/HermiteFit_%3A_fast-fitting_atomic_structures_into_a_low-resolution_density_map_using_three-dimensional_orthogonal_Hermite_functions.pdf BibTex
titre
X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism
auteur
Przemyslaw Nogly, Ivan Yu. Gushchin, Alina Remeeva, Ana M. Esteves, Nuno Borges, Pikyee Ma, Andrii Ishchenko, Sergei Grudinin, Ekaterina Round, Isabel Moraes, Valentin Borshchevskiy, Helena Santos, Valentin I. Gordeliy, Margarida Archer
article
Nature Communications, Nature Publishing Group, 2014, 5, pp.Article number: 4169. 〈10.1038/ncomms5169〉
DOI
DOI : 10.1038/ncomms5169
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titre
Rapid determination of RMSDs corresponding to macromolecular rigid body motions
auteur
Petr Popov, Sergei Grudinin
article
Journal of Computational Chemistry, Wiley, 2014, 35 (12), pp.950-956. 〈10.1002/jcc.23569〉
DOI
DOI : 10.1002/jcc.23569
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-00952248/file/JCC_RMSD_final.pdf BibTex
titre
Unique DC-SIGN Clustering Activity of a Small Glycomimetic: A Lesson for Ligand Design
auteur
Ieva Sutkeviciute, Michel Thépaut, Sara Sattin, Angela Berzi, John Mcgeagh, Sergei Grudinin, Jörg Weiser, Aline Le Roy, Jose J. Reina, Javier Rojo, Mario Clerici, Anna Bernadi, Christine Ebel, Franck Fieschi
article
ACS Chemical Biology, American Chemical Society, 2014, 9 (6), pp.1377-1385. 〈10.1021/cb500054h〉
DOI
DOI : 10.1021/cb500054h
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titre
Blind prediction of interfacial water positions in CAPRI
auteur
Marc F. Lensink, Aiain H. Moal, Paul A. Bates, Panagiotis L. Kastritis, Adrien S. J. Melquiond, Ezgi Karaca, Christophe Schmitz, Marc Van Dijk, Alexandre Bonvin, Miriam Eisenstein, Brian Jiménez-Garcí, Solène Grosdidier, Albert Solernou, Laura Pérez-Cano, Chiara Pallar, Juan Fernández-Recio, Jianqing Xu, Pravin Muthu, Krishna Praneeth Kilambi, Jeffrey Gray, Sergei Grudinin, Georgy Derevyanko, Julie Mitchell, John Wieting, Eiji Kanamori, Yuko Tsuchiya, Yoichi Murakami, Joy Sarmiento, Daron Standley, Matsuyuki Shirota, Kengo Kinoshita, Haruki Nakamura, Matthieu Chavent, Hahnbeom Park, Junsu Ko, Hasup Lee, Chaok Seok, Yang Shen, Dima Kozakov, Sandor Vajda, Petras Kundrotas, Ilya Vakser, Brian Pierce, Howook Hwang, Thom Vreven, Zhiping Weng, Idit Buch, Efrat Farkash, Haim Wolfson, Martin Zacharias, Sanbo Qin, Huan-Xiang Zhou, Shen-You Huang, Xiaoqin Zou, Justyna Wojdyla, Colin Kleanthous, Shoshana Wodak
article
Proteins – Structure, Function and Bioinformatics, Wiley, 2014, 82 (4), pp.620-632. 〈10.1002/prot.24439〉
DOI
DOI : 10.1002/prot.24439
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titre
DockTrina: Docking triangular protein trimers
auteur
Petr Popov, David Ritchie, Sergei Grudinin
article
Proteins: Structure, Function, and Genetics, Wiley, 2014, 82 (1), pp.34-44. 〈10.1002/prot.24344〉
DOI
DOI : 10.1002/prot.24344
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2013

Journal articles

titre
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
auteur
Rocco Moretti, Sarel J Fleishman, Rudi Agius, Mieczyslaw Torchala, Paul A. Bates, Panagiotis L Kastritis, João P. G. L. M. Rodrigues, Mikael Trellet, Alexandre M. J. J. Bonvin, Meng Cui, Marianne Rooman, Dimitri Gillis, Yves Dehouck, Iain Moal, Miguel Romero-Durana, Laura Pérez-Cano, Chiara Pallara, Brian Jimenez, Juan Fernández-Recio, Samuel C Flores, Michael Pacella, Krishna Praneeth Kilambi, Jeffrey J Gray, Petr Popov, Sergei Grudinin, Juan Esquivel-Rodríguez, Daisuke Kihara, Nan Zhao, Dmitry Korkin, Xiaolei Zhu, Omar N A Demerdash, Julie Mitchell, Eiji Kanamori, Yuko Tsuchiya, Haruki Nakamura, Hasup Lee, Hahnbeom Park, Chaok Seok, Jamica Sarmiento, Shide Liang, Shusuke Teraguchi, Daron M Standley, Hiromitsu Shimoyama, Genki Terashi, Mayuko Takeda-Shitaka, Mitsuo Iwadate, Hideaki Umeyama, Dmitri Beglov, David R Hall, Dima Kozakov, Sandor Vajda, Brian G Pierce, Howook Hwang, Thom Vreven, Zhiping Weng, Yangyu Huang, Haotian Li, Xiufeng Yang, Xiaofeng Ji, Shiyong Liu, Yi Xiao, Martin Zacharias, Sanbo Qin, Huan-Xiang Zhou, Sheng-You Huang, Xiaoqin Zou, Sameer Velankar, Joel Janin, Shoshana J Wodak, David Baker
article
Proteins – Structure, Function and Bioinformatics, Wiley, 2013, 81 (11), pp.1980 – 1987. 〈10.1002/prot.24356〉
DOI
DOI : 10.1002/prot.24356
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titre
Two distinct states of the HAMP domain from sensory rhodopsin transducer observed in unbiased molecular dynamics simulations.
auteur
Ivan Yu. Gushchin, Valentin I. Gordeliy, Sergei Grudinin
article
PLoS ONE, Public Library of Science, 2013, 8 (7), pp.e66917
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titre
Two Distinct States of the HAMP Domain from Sensory Rhodopsin Transducer Observed in Unbiased Molecular Dynamics Simulations
auteur
Ivan Yu. Gushchin, Valentin I. Gordeliy, Sergei Grudinin
article
PLoS ONE, Public Library of Science, 2013, 8 (7), pp.e66917. 〈10.1371/journal.pone.0066917〉
DOI
DOI : 10.1371/journal.pone.0066917
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00881143/file/IGushchin2013TwoDistinctStatesoftheHAMPDomain_journal.pone.0066917.pdf BibTex
titre
Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer
auteur
Andrii Ishchenko, Ekaterina Round, Valentin Borshchevskiy, Sergei Grudinin, Ivan Yu. Gushchin, Johann P. Klare, Taras Balandin, Alina Remeeva, Martin Engelhard, Georg Büldt, Valentin I. Gordeliy
article
Journal of Photochemistry and Photobiology B: Biology, Elsevier, 2013, 123, pp.55-58. 〈10.1016/j.jphotobiol.2013.03.008〉
DOI
DOI : 10.1016/j.jphotobiol.2013.03.008
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00881553/file/A_Ishchenko_et_al_Ground_State_Structure_of_D75N_Mutant_of_Sensory_Rhodopsin_II_2013.pdf BibTex
titre
Block-Adaptive Quantum Mechanics: An Adaptive Divide-and-Conquer Approach to Interactive Quantum Chemistry
auteur
Maël Bosson, Sergei Grudinin, Stephane Redon
article
Journal of Computational Chemistry, Wiley, 2013, 34 (6), pp.492-504. 〈10.1002/jcc.23157〉
DOI
DOI : 10.1002/jcc.23157
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2012

Journal articles

titre
A Novel Dimerization Interface of Cyclic Nucleotide Binding Domain, which is Disrupted in Presence of cAMP: Implications for CNG Channels Gating
auteur
Ivan Yu. Gushchin, Valentin I. Gordeliy, Sergei Grudinin
article
Journal of Molecular Modeling, Springer Verlag (Germany), 2012, 18 (9), pp.4053-4060. 〈10.1007/s00894-012-1404-5〉
DOI
DOI : 10.1007/s00894-012-1404-5
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00766015/file/A_novel.pdf BibTex
titre
Interactive physically-based structural modeling of hydrocarbon systems
auteur
Maël Bosson, Sergei Grudinin, Xavier Bouju, Stephane Redon
article
Journal of Computational Physics, Elsevier, 2012, 231 (6), pp.2581-2598. 〈10.1016/j.jcp.2011.12.006〉
DOI
DOI : 10.1016/j.jcp.2011.12.006
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00755542/file/HydrocarbonPrototyping.pdf BibTex
titre
Interactive quantum chemistry: A divide-and-conquer ASED-MO method
auteur
Maël Bosson, Caroline Richard, Antoine Plet, Sergei Grudinin, Stephane Redon
article
Journal of Computational Chemistry, Wiley, 2012, 33 (7), pp.779-790. 〈10.1002/jcc.22905〉
DOI
DOI : 10.1002/jcc.22905
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2011

Journal articles

titre
A comparison of neighbor search algorithms for large rigid molecules
auteur
Svetlana Artemova, Sergei Grudinin, Stephane Redon
article
Journal of Computational Chemistry, Wiley, 2011, 32 (13), pp.2865-2877. 〈10.1002/jcc.21868〉
DOI
DOI : 10.1002/jcc.21868
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titre
Active State of Sensory Rhodopsin II: Structural determinants for signal transfer and proton pumping
auteur
Ivan Yu. Gushchin, Anastasia Reshetnyak, Valentin Borshchevskiy, Andrii Ishchenko, Ekaterina Round, Sergei Grudinin, Martin Engelhard, Georg Büldt, Valentin I. Gordeliy
article
Journal of Molecular Biology, Elsevier, 2011, 412 (4), pp.591-600. 〈10.1016/j.jmb.2011.07.022〉
DOI
DOI : 10.1016/j.jmb.2011.07.022
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00766090/file/110623_NpSRII_manuscript_final.pdf BibTex
titre
Fast construction of assembly trees for molecular graphs
auteur
Svetlana Artemova, Sergei Grudinin, Stephane Redon
article
Journal of Computational Chemistry, Wiley, 2011, 32 (8), pp.1589-1598. 〈10.1002/jcc.21738〉
DOI
DOI : 10.1002/jcc.21738
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2010

Journal articles

titre
Role of the HAMP Domain Region of Sensory Rhodopsin Transducers in Signal Transduction
auteur
Ivan Yu. Gushchin, Valentin I. Gordeliy, Sergei Grudinin
article
Biochemistry, American Chemical Society, 2010, 50 (4), pp.574-580. 〈10.1021/bi101032a〉
DOI
DOI : 10.1021/bi101032a
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https://hal.inria.fr/hal-00784550/file/Role_of_the_HAMP_domain_region_of_sensory_rhodopsin_transducers_in_signal_transduction.pdf BibTex
titre
Practical modeling of molecular systems with symmetries
auteur
Sergei Grudinin, Stephane Redon
article
Journal of Computational Chemistry, Wiley, 2010, 31 (9), pp.1799-1814. 〈10.1002/jcc.21434〉
DOI
DOI : 10.1002/jcc.21434
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2005

Journal articles

titre
Water molecules and hydrogen-bonded networks in bacteriorhodopsin—molecular dynamics simulations of the ground state and the M-intermediate
auteur
Sergei Grudinin, Georg Büldt, Valentin Gordeliy, Artur Baumgaertner
article
Biophysical Journal, Biophysical Society, 2005, 88 (5), pp.3252–3261. 〈http://www.sciencedirect.com/science/article/pii/S0006349505733762〉. 〈10.1529/biophysj.104.047993〉
DOI
DOI : 10.1529/biophysj.104.047993
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  • K. Wood, S. Grudinin, B. Kessler, M. Weik, M. Johnson, G. Kneller, D. Oesterhelt, and J. Zaccai. “Dynamical heterogeneity of specific amino acids in bacteriorhodopsin”. J Mol Biol, 380: 581-591, 2008. Full text
  • S. Grudinin and A. Baumgaertner. “Boundary element method with parametrically defined surfaces”. NIC Series Volume 36: From Computational Biophysics to Systems Biology, pages 129-132, 2007. Full text

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