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

Group leader of the Nano-D team.

Coordinator of the FlexMol Inria associate team, 2019 – 2020, with ChaconLab at IQFR-CSIC, Madrid, Spain (PI Pablo Chacon). The goal of the team is to advance algorithms for multiscale macromolecular flexibility

Previously coordinated 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 was 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 CNRS research associate (CR) scientist in the Nano-D CNRS-Inria 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.

Download Resume

Software packages

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

Scientific interests

AI:

Geometric learning for structures of molecules in 3D
Representation learning of molecules
Deep learning in 3D

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 for protein-protein and protein-ligand interactions.
Docking algorithms.

Fast electrostatics:

Development of fast multipole algorithms.

Solvation:

Solvation effects based on Boundary Element Method.

Symmetry:

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

Multiscale modelling:

Adaptive algorithms for molecular modeling.
Adaptive fast electrostatics solvers.

Representative Publications

David W Ritchie and Sergei Grudinin. Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry. Journal of Applied Crystallography, 49(1):158–167, 2016. Full text
A. Hoffmann and S. Grudinin. NOLB: Nonlinear rigid block normal-mode analysis method. J Chem Theory Comput, vol. 13, pp. 2123–2134, 2017. Full text
G. Pagès and S. Grudinin. Analytical symmetry detection in protein assemblies. II. Dihedral and cubic symmetries. J Struct Biol, vol. 203, pp. 185–194, 2018. Full text

Recent Publications

Publications HAL de sergei grudinin

2024

Preprints, Working Papers, …

titre: Explaining Conformational Diversity in Protein Families through Molecular Motions
auteur: Valentin Lombard, Sergei Grudinin, Elodie Laine
article: 2024
Accès au texte intégral et bibtex

titre: Voronota-LT: efficient, flexible and solvent-aware tessellation-based analysis of atomic interactions
auteur: Kliment Olechnovič, Sergei Grudinin
article: 2024
Accès au texte intégral et bibtex

2023

Journal articles

titre: Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data
auteur: Sri Devan Appasamy, John Berrisford, Romana Gaborova, Sreenath Nair, Sergei Grudinin, David Armstrong, Ivanna Pidruchna, Joseph I J Ellaway, Grisell Díaz Leines, Deepti Gupta, Deborah Harrus, Mihaly Varadi, Sameer Velankar
article: Scientific Data , 2023, 10, pp.853. ⟨10.1038/s41597-023-02778-9⟩
DOI: DOI : 10.1038/s41597-023-02778-9
Accès au texte intégral et bibtex

titre: Stages of OCP–FRP Interactions in the Regulation of Photoprotection in Cyanobacteria, Part 2: Small-Angle Neutron Scattering with Partial Deuteration
auteur: Maksym Golub, Marcus Moldenhauer, Olga Matsarskaia, Anne Martel, Sergei Grudinin, Dmytro Soloviov, Alexander Kuklin, Eugene Maksimov, Thomas Friedrich, Jörg Pieper
article: Journal of Physical Chemistry B, 2023, 127 (9), pp.1901-1913. ⟨10.1021/acs.jpcb.2c07182⟩
DOI: DOI : 10.1021/acs.jpcb.2c07182
Accès au bibtex

2022

Journal articles

titre: Docking-based long timescale simulation of cell-size protein systems at atomic resolution
auteur: Ilya A Vakser, Sergei Grudinin, Nathan W Jenkins, Petras J Kundrotas, Eric J Deeds
article: Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (41), pp.e2210249119:1-8. ⟨10.1073/pnas.2210249119⟩
DOI: DOI : 10.1073/pnas.2210249119
Accès au texte intégral et bibtex

titre: 3D time-lapse imaging of a mouse embryo using intensity diffraction tomography embedded inside a deep learning framework
auteur: William Pierré, Lionel Hervé, Chiara Paviolo, Ondrej Mandula, Vincent Remondiere, Sophie Morales, Sergei Grudinin, Pierre Ray, Magali Dhellemmes, Christophe Arnoult, Cédric Allier
article: Applied optics, 2022, 61 (12), pp.3337. ⟨10.1364/AO.453910⟩
DOI: DOI : 10.1364/AO.453910
Accès au bibtex

Conference papers

titre: 3D live cell imaging of whole organoids in time-lapse using intensity diffraction tomography
auteur: William Pierré, Lionel Hervé, Cédric Allier, Sophie Morales, Sergei Grudinin, Pierre F. Ray, Christophe Arnoult, Magali Dhellemmes
article: SPIE Photonics Europe, Apr 2022, Strasbourg, France. ⟨10.1117/12.2625734⟩
DOI: DOI : 10.1117/12.2625734
Accès au bibtex

titre: 6DCNN with roto-translational convolution filters for volumetric data processing
auteur: Dmitrii Zhemchuzhnikov, Ilia Igashov, Sergei Grudinin
article: The Thirty-Sixth AAAI Conference on Artificial Intelligence (AAAI-22), AAAI, Feb 2022, Vancouver, Canada. pp.4707-4715
Accès au texte intégral et bibtex

titre: Session introduction: AI-driven Advances in Modeling of Protein Structure
auteur: Krzysztof Fidelis, Sergei Grudinin
article: Pacific Symposium on Biocomputing 2022, Jan 2022, Fairmont Orchid – Hawaii, United States
Accès au texte intégral et bibtex

2021

Journal articles

titre: Protein sequence-to-structure learning: Is this the end(-to-end revolution)?
auteur: Elodie Laine, Stephan Eismann, Arne Elofsson, Sergei Grudinin
article: Proteins – Structure, Function and Bioinformatics, 2021, 89 (12), pp.1770-1786. ⟨10.1002/prot.26235⟩
DOI: DOI : 10.1002/prot.26235
Accès au texte intégral et bibtex

titre: Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
auteur: Andriy Kryshtafovych, John Moult, Wendy M Billings, Dennis Della Corte, Krzysztof Fidelis, Sohee Kwon, Kliment Olechnovič, Chaok Seok, Česlovas Venclovas, Jonghun Won, Badri Adhikari, Recep Adiyaman, Joaquim Aguirre-Plans, Ivan Anishchenko, Minkyung Baek, David Baker, Frederico Baldassarre, Jacob Barger, Sutanu Bhattacharya, Debswapna Bhattacharya, Mor Bitton, Renzhi Cao, Jianlin Cheng, Charles Christoffer, Cezary Czaplewski, Arne Elofsson, Eshel Faraggi, Michael Feig, Narcis Fernandez-Fuentes, Nick Grishin, Sergei Grudinin, Zhiye Guo, Yuya Hanazono, Demis Hassabis, Bryce Hedelius, Lim Heo, Naozumi Hiranuma, Cassandra Hunt, Ilia Igashov, Takashi Ishida, Robert L. Jernigan, David Jones, John Jumper, Maria Kadukova, Shaun Kandathil, Chen Keasar, Daisuke Kihara, Lisa Kinch, Yasuomi Kiyota, Andrzje Kloczkowski, Pushmeet Kohli, Mateusz Kogut, Elodie Laine, Cade Lilley, Jian Liu, Adam Liwo, Emilia Lubecka, Arup Mondal, Connor J. Morris, Liam Mcguffin, Alexis Molina, Tsukasa Nakamura, Baldo Oliva, Alberto Perez, Gabriele Pozzati, Daipayan Sarkar, Rin Sato, Torsten Schwede, Bikash Shrestha, Tomer Sidi, Gabriel Studer, Md Hossain Shuvo, Mayuko Takeda-Shitaka, Yuma Takei, Genki Terashi, Kentaro Tomii, Yuko Tsuchiya, Kathryn Tunyasuvunakool, Björn Waliner, Tianqi Wu, Jinbo Xu, Yu Yamamori, Chengxin Zhang, Yang Zhang, Wei Zheng
article: Proteins – Structure, Function and Bioinformatics, 2021, 89 (12), pp.1987-1996. ⟨10.1002/prot.26231⟩
DOI: DOI : 10.1002/prot.26231
Accès au texte intégral et bibtex

titre: Pepsi-SAXS/SANS -small-angle scattering-guided tools for integrative structural bioinformatics
auteur: Sergei Grudinin, Anne Martel, Sylvain Prevost
article: Acta Crystallographica Section A : Foundations and Advances [2014-..], 2021, 77 (A2), pp.C49. ⟨10.1107/S0108767321096288⟩
DOI: DOI : 10.1107/S0108767321096288
Accès au texte intégral et bibtex

titre: Deep learning entering the post-protein structure prediction era : new horizons for structural biology
auteur: Sergei Grudinin
article: Acta Crystallographica Section A : Foundations and Advances [2014-..], 2021, A77 (C473), ⟨10.1107/S0108767321092138⟩
DOI: DOI : 10.1107/S0108767321092138
Accès au texte intégral et bibtex

titre: Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
auteur: Marc Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael Chaleil, Tereza Clarence, Paul Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Agnieszka Lipska, Adam Liwo, Emilia Lubecka, Martyna Maszota‐zieleniak, Adam Sieradzan, Rafał Ślusarz, Patryk Wesołowski, Karolina Zięba, Carlos del Carpio Muñoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey Gray, Alexandre Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jiménez‐garcía, Panagiotis Koukos, Siri van Keulen, Charlotte van Noort, Manon Réau, Jorge Roel‐touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis Rodríguez‐lumbreras, Juan Fernandez‐recio, Agnieszka Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng‐you Huang, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan Guest, Rui Yin, Ghazaleh Taherzadeh, Brian Pierce, Didier Barradas‐bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda‐shitaka, Petras Kundrotas, Amar Singh, Ilya Vakser, Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana Wodak
article: Proteins – Structure, Function and Bioinformatics, 2021, 89 (12), pp.1800-1823. ⟨10.1002/prot.26222⟩
DOI: DOI : 10.1002/prot.26222
Accès au texte intégral et bibtex

titre: KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions
auteur: Maria Kadukova, Karina dos Santos Machado, Pablo Chacón, Sergei Grudinin
article: Bioinformatics, 2021, 37 (7), pp.943-950. ⟨10.1093/bioinformatics/btaa748⟩
DOI: DOI : 10.1093/bioinformatics/btaa748
Accès au texte intégral et bibtex

titre: HOPMA: Boosting protein functional dynamics with colored contact maps
auteur: Elodie Laine, Sergei Grudinin
article: Journal of Physical Chemistry B, 2021, 125 (10), pp.2577-2588. ⟨10.1021/acs.jpcb.0c11633⟩
DOI: DOI : 10.1021/acs.jpcb.0c11633
Accès au texte intégral et bibtex

titre: VoroCNN: Deep convolutional neural network built on 3D Voronoi tessellation of protein structures
auteur: Ilia Igashov, Kliment Olechnovic, Maria Kadukova, Česlovas Venclovas, Sergei Grudinin
article: Bioinformatics, 2021, 37 (16), pp.2332-2339. ⟨10.1093/bioinformatics/btab118⟩
DOI: DOI : 10.1093/bioinformatics/btab118
Accès au texte intégral et bibtex

titre: Spherical convolutions on molecular graphs for protein model quality assessment
auteur: Ilia Igashov, Nikita Pavlichenko, Sergei Grudinin
article: Machine Learning: Science and Technology, 2021, ⟨10.1088/2632-2153/abf856⟩
DOI: DOI : 10.1088/2632-2153/abf856
Accès au texte intégral et bibtex

Conference papers

titre: Deep learning framework applied to optical diffraction tomography (ODT)
auteur: William Pierré, Lionel Hervé, Cédric Allier, Sophie Morales, Sergei Grudinin, Shwetadwip Chowdhury, Laura Waller, Christophe Arnoult, Pierre Ray, Magali Dhellemmes
article: Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVIII, SPIE, Mar 2021, Online Only, France. pp.1, ⟨10.1117/12.2582361⟩
DOI: DOI : 10.1117/12.2582361
Accès au bibtex

Preprints, Working Papers, …

titre: Convex-PL-R – Revisiting affinity predictions and virtual screening using physics-informed machine learning
auteur: Maria Kadukova, Vladimir Chupin, Sergei Grudinin
article: 2021
Accès au texte intégral et bibtex

2020

Journal articles

titre: Hydroxylation of antitubercular drug candidate, SQ109, by mycobacterial cytochrome P450
auteur: Sergey Bukhdruker, Tatsiana Varaksa, Irina Grabovec, Egor Marin, Polina Shabunya, Maria Kadukova, Sergei Grudinin, Anton Kavaleuski, Anastasiia Gusach, Andrei Gilep, Valentin Borshchevskiy, Natallia Strushkevich
article: International Journal of Molecular Sciences, 2020, ⟨10.1101/2020.08.27.269936⟩
DOI: DOI : 10.1101/2020.08.27.269936
Accès au bibtex

titre: Interdomain Flexibility within NADPH Oxidase Suggested by SANS Using LMNG Stealth Carrier
auteur: Annelise Vermot, Isabelle Petit-Härtlein, Cécile Breyton, Aline Le Roy, Michel Thépaut, Corinne Vivès, Martine Moulin, Michael Härtlein, Sergei Grudinin, Susan M E Smith, Christine Ebel, Anne Martel, Franck Fieschi
article: Biophysical Journal, 2020, 119 (3), pp.605-618. ⟨10.1016/j.bpj.2020.06.025⟩
DOI: DOI : 10.1016/j.bpj.2020.06.025
Accès au texte intégral et bibtex

titre: Predicting protein functional motions: an old recipe with a new twist
auteur: Sergei Grudinin, Elodie Laine, Alexandre Hoffmann
article: Biophysical Journal, 2020, 118 (10), pp.2513-2525. ⟨10.1016/j.bpj.2020.03.020⟩
DOI: DOI : 10.1016/j.bpj.2020.03.020
Accès au texte intégral et bibtex

titre: Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution
auteur: Andreas Haahr Larsen, Yong Wang, Alessandro Bottaro, Sergei Grudinin, Lise Arleth, Kresten Lindorff-Larsen
article: PLoS Computational Biology, 2020, 16 (4), pp.e1007870. ⟨10.1371/journal.pcbi.1007870⟩
DOI: DOI : 10.1371/journal.pcbi.1007870
Accès au bibtex

titre: Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4
auteur: Maria Kadukova, Vladimir Chupin, Sergei Grudinin
article: Journal of Computer-Aided Molecular Design, 2020, 34, pp.191-200. ⟨10.1007/s10822-019-00263-3⟩
DOI: DOI : 10.1007/s10822-019-00263-3
Accès au texte intégral et bibtex

Book sections

titre: AnAnaS: Software for Analytical Analysis of Symmetries in Protein Structures
auteur: Guillaume Pagès, Sergei Grudinin
article: Protein Structure Prediction. Methods in Molecular Biology, pp.245-257, 2020, ⟨10.1007/978-1-0716-0708-4_14⟩
DOI: DOI : 10.1007/978-1-0716-0708-4_14
Accès au texte intégral et bibtex

2019

Journal articles

titre: DeepSymmetry : Using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures
auteur: Guillaume Pagès, Sergei Grudinin
article: Bioinformatics, 2019, 35 (24), pp.5113-5120. ⟨10.1093/bioinformatics/btz454⟩
DOI: DOI : 10.1093/bioinformatics/btz454
Accès au texte intégral et bibtex

titre: Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
auteur: Jorge Eduardo Fajardo, Rojan Shrestha, Nelson Gil, Adam Belsom, Silvia Crivelli, Cezary Czaplewski, Krzysztof Fidelis, Sergei Grudinin, Mikhail Karasikov, Agnieszka Karczyńska, Andriy Kryshtafovych, Alexander Leitner, Adam Liwo, Emilia Lubecka, Bohdan Monastyrskyy, Guillaume Pagès, Juri Rappsilber, Adam Sieradzan, Celina Sikorska, Esben Trabjerg, Andras Fiser
article: Proteins – Structure, Function and Bioinformatics, 2019, Critical Assessment of Methods of Protein Structure Prediction (CASP) Special Issue, 87 (12), pp.1283-1297. ⟨10.1002/prot.25816⟩
DOI: DOI : 10.1002/prot.25816
Accès au bibtex

titre: Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences
auteur: Greg Hura, Curtis Hodge, Daniel Rosenberg, Dmytro Guzenko, Jose Duarte, Bohdan Monastyrskyy, Sergei Grudinin, Andriy Kryshtafovych, John Tainer, Krzysztof Fidelis, Susan Tsutakawa
article: Proteins – Structure, Function and Bioinformatics, 2019, Critical Assessment of Methods of Protein Structure Prediction (CASP) Special Issue, 87 (12), pp.1298-1314. ⟨10.1002/prot.25827⟩
DOI: DOI : 10.1002/prot.25827
Accès au bibtex

titre: Controlled‐advancement rigid‐body optimization of nanosystems
auteur: Petr Popov, Sergei Grudinin, Andrii Kurdiuk, Pavel Buslaev, Stephane Redon
article: Journal of Computational Chemistry, 2019, 40 (27), pp.2391-2399. ⟨10.1002/jcc.26016⟩
DOI: DOI : 10.1002/jcc.26016
Accès au bibtex

titre: Blind prediction of homo‐ and hetero‐ protein complexes: The CASP13‐CAPRI experiment
auteur: Marc Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphaël A.G. Chaleil, Tereza Gerguri, Paul Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran‐ran Liu, Xi‐ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Paweł Krupa, Magdalena Mozolewska, Łukasz Golon, Sergey Samsonov, Adam Liwo, Silvia Crivelli, Guillaume Pagès, Mikhail Karasikov, Maria Kadukova, Yumeng Yan, Sheng‐you Huang, Mireia Rosell, Luis Angel Rodríguez‐lumbreras, Miguel Romero‐durana, Lucía Díaz‐bueno, Juan Fernandez‐recio, Charles Christoffer, Genki Terashi, Woong‐hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subram, Daisuke Kihara, Dima Kozakov, Sandor Vajda, Kathyn Porter, Dzmitry Padhorny, Israel Desta, Dmitri Beglov, Mikhail Ignatov, Sergey Kotelnikov, Iain Moal, David Ritchie, Isaure Chauvot de Beauchêne, Bernard Maigret, Marie-Dominique Devignes, Maria Elisa Ruiz Echartea, Didier Barradas‐bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yue Cao, Yang Shen, Minkyung Baek, Taeyong Park, Hyeonuk Woo, Chaok Seok, Merav Braitbard, Lirane Bitton, Dina Scheidman‐duhovny, Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas, Petras J. Kundrotas, Saveliy Belkin, Devlina Chakravarty, Varsha Badal, Ilya A. Vakser, Thom Vreven, Sweta Vangaveti, Tyler M. Borrman, Zhiping Weng, Johnathan D Guest, Ragul Gowthaman, Brian G Pierce, Xianjin Xu, Rui Duan, Liming Qiu, Jie Hou, Benjamin Ryan Merideth, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Panos Koukos, Jorge Roel‐touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael Trellet, Adrien S.J. Melquiond, Li Xue, Brian Jiménez‐garcía, Charlotte Noort, Rodrigo Honorato, Alexandre M.J.J. Bonvin, Shoshana J. Wodak
article: Proteins – Structure, Function and Bioinformatics, 2019, 87 (12), pp.1200-1221. ⟨10.1002/prot.25838⟩
DOI: DOI : 10.1002/prot.25838
Accès au texte intégral et bibtex

titre: Protein model quality assessment using 3D oriented convolutional neural networks
auteur: Guillaume Pagès, Benoit Charmettant, Sergei Grudinin
article: Bioinformatics, 2019, 35 (18), pp.3313-3319. ⟨10.1093/bioinformatics/btz122⟩
DOI: DOI : 10.1093/bioinformatics/btz122
Accès au texte intégral et bibtex

titre: KAP1 is an antiparallel dimer with a functional asymmetry
auteur: Giulia Fonti, Maria Marcaida, Louise Bryan, Sylvain Träger, Alexandra Kalantzi, Pierre-Yves Jl Helleboid, Davide Demurtas, Mark Tully, Sergei Grudinin, Didier Trono, Beat Fierz, Matteo Dal Peraro
article: Life Science Alliance, 2019, 2 (4), pp.e201900349. ⟨10.26508/lsa.201900349⟩
DOI: DOI : 10.26508/lsa.201900349
Accès au bibtex

titre: Smooth orientation-dependent scoring function for coarse-grained protein quality assessment
auteur: Mikhail Karasikov, Guillaume Pagès, Sergei Grudinin
article: Bioinformatics, 2019, 35 (16), pp.2801-2808. ⟨10.1093/bioinformatics/bty1037⟩
DOI: DOI : 10.1093/bioinformatics/bty1037
Accès au texte intégral et bibtex

2018

Journal articles

titre: Deep convolutional networks for quality assessment of protein folds
auteur: Georgy Derevyanko, Sergei Grudinin, Yoshua Bengio, Guillaume Lamoureux
article: Bioinformatics, 2018, 34 (23), pp.4046-4053. ⟨10.1093/bioinformatics/bty494⟩
DOI: DOI : 10.1093/bioinformatics/bty494
Accès au bibtex

titre: Analytical symmetry detection in protein assemblies. II. Dihedral and Cubic symmetries
auteur: Guillaume Pagès, Sergei Grudinin
article: Journal of Structural Biology, 2018, 203 (3), pp.185-194. ⟨10.1016/j.jsb.2018.05.005⟩
DOI: DOI : 10.1016/j.jsb.2018.05.005
Accès au texte intégral et bibtex

titre: RapidRMSD: Rapid determination of RMSDs corresponding to motions of flexible molecules
auteur: Emilie Neveu, Petr Popov, Alexandre Hoffmann, Angelo Migliosi, Xavier Besseron, Gregoire Danoy, Pascal Bouvry, Sergei Grudinin
article: Bioinformatics, 2018, 34 (16), pp.2757-2765. ⟨10.1093/bioinformatics/bty160⟩
DOI: DOI : 10.1093/bioinformatics/bty160
Accès au texte intégral et bibtex

titre: Analytical symmetry detection in protein assemblies. I. Cyclic symmetries
auteur: Guillaume Pagès, Elvira Kinzina, Sergei Grudinin
article: Journal of Structural Biology, 2018, 203 (2), pp.142-148. ⟨10.1016/j.jsb.2018.04.004⟩
DOI: DOI : 10.1016/j.jsb.2018.04.004
Accès au texte intégral et bibtex

titre: Eurecon: Equidistant Uniform Rigid-body Ensemble Constructor
auteur: Petr Popov, Sergei Grudinin
article: Journal of Molecular Graphics and Modelling, 2018, 80, pp.313-319. ⟨10.1016/j.jmgm.2018.01.015⟩
DOI: DOI : 10.1016/j.jmgm.2018.01.015
Accès au texte intégral et 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, 2018, 32 (1), pp.151-162. ⟨10.1007/s10822-017-0062-1⟩
DOI: DOI : 10.1007/s10822-017-0062-1
Accès au texte intégral et bibtex

Preprints, Working Papers, …

titre: User Guide for NOLB : Non-Linear Normal Mode Analysis
auteur: Sergei Grudinin
article: 2018
Accès au texte intégral et bibtex

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, 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

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, 2017, 50 (4), pp.1036-1047. ⟨10.1107/S1600576717008172⟩
DOI: DOI : 10.1107/S1600576717008172
Accès au texte intégral et bibtex

titre: Mechanism of transmembrane signaling by sensor histidine kinases
auteur: Ivan Yu. Gushchin, Igor I 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, 2017, 356 (6342), pp.eaah6345. ⟨10.1126/science.aah6345⟩
DOI: DOI : 10.1126/science.aah6345
Accès au texte intégral et 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 : Structural biology [1993-..], 2017, D73, pp.449 – 464. ⟨10.1107/S2059798317005745⟩
DOI: DOI : 10.1107/S2059798317005745
Accès au texte intégral et bibtex

titre: NOLB: Nonlinear Rigid Block Normal Mode Analysis Method
auteur: Alexandre Hoffmann, Sergei Grudinin
article: Journal of Chemical Theory and Computation, 2017, 13 (5), pp.2123-2134. ⟨10.1021/acs.jctc.7b00197⟩
DOI: DOI : 10.1021/acs.jctc.7b00197
Accès au texte intégral et 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 W Ghoorah, Sergei Grudinin, David Ritchie
article: Proteins: Structure, Function, and Genetics, 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

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, 2017, 7, pp.41811. ⟨10.1038/srep41811⟩
DOI: DOI : 10.1038/srep41811
Accès au texte intégral et 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

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 A.G. Chaleil, Paul A Bates, Efrat Ben-Zeev, Miriam Eisenstein, Surendra Negi S., Thom Vreven, Brian G Pierce, Tyler M. Borrman, Jinchao Yu, Françoise Ochsenbein, Zhiping Weng, Raphaël Guérois, Anna Vangone, João P.G.L.M. Rodrigues, Gydo van Zundert, Mehdi Nellen, Li Xue, Ezgi Karaca, Adrien S. J. Melquiond, Koen Visscher, Panagiotis L Kastritis, Alexandre M. J. J. Bonvin, Xianjin Xu, Liming Qiu, Chengfei Yan, Jilong Li, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Yang Sheng, Lenna X. Peterson, Hyung-Rae Kim, Amit Roy, Xusi Han, Juan Esquivel-Rodríguez, Daisuke Kihara, Xiaofeng Yu, Neil J. Bruce, Jonathan C. Fuller, Rebbecca C. Wade, Ivan Anishchenko, Petras J. Kundrotas, Ilya A. 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 R. Hall, Dmitri Beglov, Artem Mamonov, Bing Xia, Tanggis Bohnuud, Carlos A. del Carpio, Eichiro Ichiishi, Nicholas Marze, Daisuke Kuroda, Shourya S. Roy Burman, Jeffrey J Gray, Edrisse Chermak, Luigi Cavallo, Romina Oliva, Andrey Tovchigrechko, Shoshana J Wodak
article: Proteins – Structure, Function and Bioinformatics, 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

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, 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

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, 2016, 32 (7), pp.i693-i701. ⟨10.1093/bioinformatics/btw443⟩
DOI: DOI : 10.1093/bioinformatics/btw443
Accès au texte intégral et 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, 2016, 56 (8), pp.1410-1419. ⟨10.1021/acs.jcim.5b00512⟩
DOI: DOI : 10.1021/acs.jcim.5b00512
Accès au texte intégral et 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, 2016, 56 (6), pp.1053-1062. ⟨10.1021/acs.jcim.5b00339⟩
DOI: DOI : 10.1021/acs.jcim.5b00339
Accès au bibtex

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, 2016, 12 (3), pp.1019-1028. ⟨10.1021/acs.jctc.5b01106⟩
DOI: DOI : 10.1021/acs.jctc.5b01106
Accès au bibtex

titre: Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry
auteur: David W. Ritchie, Sergei Grudinin
article: Journal of Applied Crystallography, 2016, 49 (1), pp.158-167. ⟨10.1107/S1600576715022931⟩
DOI: DOI : 10.1107/S1600576715022931
Accès au texte intégral et 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
Accès au texte intégral et 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
Accès au texte intégral et 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, 2015, 55 (10), pp.2242-2255. ⟨10.1021/acs.jcim.5b00372⟩
DOI: DOI : 10.1021/acs.jcim.5b00372
Accès au texte intégral et bibtex

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

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 : Structural biology [1993-..], 2014, 70 (8), pp.2069-2084. ⟨10.1107/S1399004714011493⟩
DOI: DOI : 10.1107/S1399004714011493
Accès au texte intégral et 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, 2014, 5, pp.Article number: 4169. ⟨10.1038/ncomms5169⟩
DOI: DOI : 10.1038/ncomms5169
Accès au bibtex

titre: Rapid determination of RMSDs corresponding to macromolecular rigid body motions
auteur: Petr Popov, Sergei Grudinin
article: Journal of Computational Chemistry, 2014, 35 (12), pp.950-956. ⟨10.1002/jcc.23569⟩
DOI: DOI : 10.1002/jcc.23569
Accès au texte intégral et 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, 2014, 9 (6), pp.1377-1385. ⟨10.1021/cb500054h⟩
DOI: DOI : 10.1021/cb500054h
Accès au bibtex

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 M. J. J. 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 J. Gray, Sergei Grudinin, Georgy Derevyanko, Julie C. Mitchell, John Wieting, Eiji Kanamori, Yuko Tsuchiya, Yoichi Murakami, Joy Sarmiento, Daron M. Standley, Matsuyuki Shirota, Kengo Kinoshita, Haruki Nakamura, Matthieu Chavent, Hahnbeom Park, Junsu Ko, Hasup Lee, Chaok Seok, Yang Shen, Dima Kozakov, Sandor Vajda, Petras J. Kundrotas, Ilya A. Vakser, Brian G. Pierce, Howook Hwang, Thom Vreven, Zhiping Weng, Idit Buch, Efrat Farkash, Haim J. Wolfson, Martin Zacharias, Sanbo Qin, Huan-Xiang Zhou, Shen-You Huang, Xiaoqin Zou, Justyna A. Wojdyla, Colin Kleanthous, Shoshana J. Wodak
article: Proteins – Structure, Function and Bioinformatics, 2014, 82 (4), pp.620-632. ⟨10.1002/prot.24439⟩
DOI: DOI : 10.1002/prot.24439
Accès au bibtex

titre: DockTrina: Docking triangular protein trimers
auteur: Petr Popov, David Ritchie, Sergei Grudinin
article: Proteins: Structure, Function, and Genetics, 2014, 82 (1), pp.34-44. ⟨10.1002/prot.24344⟩
DOI: DOI : 10.1002/prot.24344
Accès au bibtex

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, 2013, 81 (11), pp.1980 – 1987. ⟨10.1002/prot.24356⟩
DOI: DOI : 10.1002/prot.24356
Accès au bibtex

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, 2013, 8 (7), pp.e66917. ⟨10.1371/journal.pone.0066917⟩
DOI: DOI : 10.1371/journal.pone.0066917
Accès au texte intégral et 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, 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

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, 2013, 34 (6), pp.492-504. ⟨10.1002/jcc.23157⟩
DOI: DOI : 10.1002/jcc.23157
Accès au bibtex

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, 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

titre: Interactive physically-based structural modeling of hydrocarbon systems
auteur: Maël Bosson, Sergei Grudinin, Xavier Bouju, Stephane Redon
article: Journal of Computational Physics, 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

titre: Interactive quantum chemistry: A divide-and-conquer ASED-MO method
auteur: Maël Bosson, Antoine Plet, Sergei Grudinin, Stephane Redon, Caroline Richard
article: Journal of Computational Chemistry, 2012, 33 (7), pp.779-790. ⟨10.1002/jcc.22905⟩
DOI: DOI : 10.1002/jcc.22905
Accès au bibtex

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, 2011, 32 (13), pp.2865-2877. ⟨10.1002/jcc.21868⟩
DOI: DOI : 10.1002/jcc.21868
Accès au bibtex

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, 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

titre: Fast construction of assembly trees for molecular graphs
auteur: Svetlana Artemova, Sergei Grudinin, Stephane Redon
article: Journal of Computational Chemistry, 2011, 32 (8), pp.1589-1598. ⟨10.1002/jcc.21738⟩
DOI: DOI : 10.1002/jcc.21738
Accès au bibtex

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, 2010, 50 (4), pp.574-580. ⟨10.1021/bi101032a⟩
DOI: DOI : 10.1021/bi101032a
Accès au texte intégral et bibtex

titre: Practical modeling of molecular systems with symmetries
auteur: Sergei Grudinin, Stephane Redon
article: Journal of Computational Chemistry, 2010, 31 (9), pp.1799-1814. ⟨10.1002/jcc.21434⟩
DOI: DOI : 10.1002/jcc.21434
Accès au bibtex

2008

Journal articles

titre: Dynamical heterogeneity of specific amino acids in bacteriorhodopsin
auteur: K. Wood, Sergei Grudinin, B. Kessler, Martin Weik, M. Johnson, Gerald R. Kneller, D. Oesterheit, Giuseppe Zaccai
article: Journal of Molecular Biology, 2008, 380 (3), pp.581-591. ⟨10.1016/j.jmb.2008.04.077⟩
DOI: DOI : 10.1016/j.jmb.2008.04.077
Accès au bibtex

2005

Journal articles

titre: Water molecules and hydrogen-bonded networks in bacteriorhodopsinmolecular dynamics simulations of the ground state and the M-intermediate
auteur: Sergei Grudinin, Georg Büldt, Valentin Gordeliy, Artur Baumgaertner
article: Biophysical Journal, 2005, 88 (5), pp.3252–3261. ⟨10.1529/biophysj.104.047993⟩
DOI: DOI : 10.1529/biophysj.104.047993
Accès au bibtex

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