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Controlled‐advancement rigid‐body optimization of nanosystems

Petr Popov , Sergei Grudinin , Andrii Kurdiuk , Pavel Buslaev , Stephane Redon
Journal of Computational Chemistry, 2019, 40 (27), pp.2391-2399. ⟨10.1002/jcc.26016⟩
Article dans une revue hal-02315276v1

Hydroxylation of antitubercular drug candidate, SQ109, by mycobacterial cytochrome P450

Sergey Bukhdruker , Tatsiana Varaksa , Irina Grabovec , Egor Marin , Polina Shabunya , et al.
International Journal of Molecular Sciences, 2020, ⟨10.1101/2020.08.27.269936⟩
Article dans une revue hal-02931707v1
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AnAnaS: Software for Analytical Analysis of Symmetries in Protein Structures

Guillaume Pagès , Sergei Grudinin
Protein Structure Prediction. Methods in Molecular Biology, pp.245-257, 2020, ⟨10.1007/978-1-0716-0708-4_14⟩
Chapitre d'ouvrage hal-02931690v1
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KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions

Maria Kadukova , Karina dos Santos Machado , Pablo Chacón , Sergei Grudinin
Bioinformatics, 2021, 37 (7), pp.943-950. ⟨10.1093/bioinformatics/btaa748⟩
Article dans une revue hal-02931666v1
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Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization

Maria Kadukova , Sergei Grudinin
Journal of Computer-Aided Molecular Design, 2017, 31 (10), pp.943-958. ⟨10.1007/s10822-017-0068-8⟩
Article dans une revue hal-01591154v1
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User Guide for AnAnaS : Analytical Analyzer of Symmetries

Guillaume Pagès , Sergei Grudinin
2017
Pré-publication, Document de travail hal-01644987v1
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Spherical convolutions on molecular graphs for protein model quality assessment

Ilia Igashov , Nikita Pavlichenko , Sergei Grudinin
Machine Learning: Science and Technology, 2021, ⟨10.1088/2632-2153/abf856⟩
Article dans une revue hal-03006448v2
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Analytical symmetry detection in protein assemblies. II. Dihedral and Cubic symmetries

Guillaume Pagès , Sergei Grudinin
Journal of Structural Biology, 2018, 203 (3), pp.185-194. ⟨10.1016/j.jsb.2018.05.005⟩
Article dans une revue hal-01816449v1
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Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer

Andrii Ishchenko , Ekaterina Round , Valentin Borshchevskiy , Sergei Grudinin , Ivan Yu. Gushchin , et al.
Journal of Photochemistry and Photobiology B: Biology, 2013, 123, pp.55-58. ⟨10.1016/j.jphotobiol.2013.03.008⟩
Article dans une revue hal-00881553v1
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Pepsi-SAXS : an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles

Sergei Grudinin , Maria Garkavenko , Andrei Kazennov
Acta crystallographica Section D : Structural biology [1993-..], 2017, D73, pp.449 - 464. ⟨10.1107/S2059798317005745⟩
Article dans une revue hal-01516719v1
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Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates

Maria Kadukova , Sergei Grudinin
Journal of Chemical Information and Modeling, 2016, 56 (8), pp.1410-1419. ⟨10.1021/acs.jcim.5b00512⟩
Article dans une revue hal-01381010v1
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New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex

Andrii Ishchenko , Ekaterina Round , Valentin Borshchevskiy , Sergei Grudinin , Ivan Yu. Gushchin , et al.
Scientific Reports, 2017, 7, pp.41811. ⟨10.1038/srep41811⟩
Article dans une revue hal-01458744v1
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Deep learning entering the post-protein structure prediction era : new horizons for structural biology

Sergei Grudinin
Acta Crystallographica Section A : Foundations and Advances [2014-..], 2021, A77 (C473), ⟨10.1107/S0108767321092138⟩
Article dans une revue hal-03874684v1
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Blind prediction of homo‐ and hetero‐ protein complexes: The CASP13‐CAPRI experiment

Marc Lensink , Guillaume Brysbaert , Nurul Nadzirin , Sameer Velankar , Raphaël A.G. Chaleil , et al.
Proteins - Structure, Function and Bioinformatics, 2019, 87 (12), pp.1200-1221. ⟨10.1002/prot.25838⟩
Article dans une revue hal-02320974v1
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Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data

Sri Devan Appasamy , John Berrisford , Romana Gaborova , Sreenath Nair , Sergei Grudinin , et al.
Scientific Data , 2023, 10, pp.853. ⟨10.1038/s41597-023-02778-9⟩
Article dans une revue hal-04304774v1

Unique DC-SIGN Clustering Activity of a Small Glycomimetic: A Lesson for Ligand Design

Ieva Sutkeviciute , Michel Thépaut , Sara Sattin , Angela Berzi , John Mcgeagh , et al.
ACS Chemical Biology, 2014, 9 (6), pp.1377-1385. ⟨10.1021/cb500054h⟩
Article dans une revue hal-01018565v1
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User Guide for NOLB : Non-Linear Normal Mode Analysis

Sergei Grudinin
2018
Pré-publication, Document de travail hal-01565129v3

Fast construction of assembly trees for molecular graphs

Svetlana Artemova , Sergei Grudinin , Stephane Redon
Journal of Computational Chemistry, 2011, 32 (8), pp.1589-1598. ⟨10.1002/jcc.21738⟩
Article dans une revue istex hal-00746836v1

Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences

Greg Hura , Curtis Hodge , Daniel Rosenberg , Dmytro Guzenko , Jose Duarte , et al.
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⟩
Article dans une revue hal-02315292v1
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Protein model quality assessment using 3D oriented convolutional neural networks

Guillaume Pagès , Benoit Charmettant , Sergei Grudinin
Bioinformatics, 2019, 35 (18), pp.3313-3319. ⟨10.1093/bioinformatics/btz122⟩
Article dans une revue hal-01899468v1

Blind prediction of interfacial water positions in CAPRI

Marc F. Lensink , Aiain H. Moal , Paul A. Bates , Panagiotis L. Kastritis , Adrien S. J. Melquiond , et al.
Proteins - Structure, Function and Bioinformatics, 2014, 82 (4), pp.620-632. ⟨10.1002/prot.24439⟩
Article dans une revue hal-00880345v1
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Mechanism of transmembrane signaling by sensor histidine kinases

Ivan Yu. Gushchin , Igor I Melkinov , Vitaly Polovinkin , Andrii Ishchenko , Anastasia Yuzhakova , et al.
Science, 2017, 356 (6342), pp.eaah6345. ⟨10.1126/science.aah6345⟩
Article dans une revue hal-01526454v1
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Rapid determination of RMSDs corresponding to macromolecular rigid body motions

Petr Popov , Sergei Grudinin
Journal of Computational Chemistry, 2014, 35 (12), pp.950-956. ⟨10.1002/jcc.23569⟩
Article dans une revue hal-00952248v1
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Predicting protein functional motions: an old recipe with a new twist

Sergei Grudinin , Elodie Laine , Alexandre Hoffmann
Biophysical Journal, 2020, 118 (10), pp.2513-2525. ⟨10.1016/j.bpj.2020.03.020⟩
Article dans une revue hal-02291552v1
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Interdomain Flexibility within NADPH Oxidase Suggested by SANS Using LMNG Stealth Carrier

Annelise Vermot , Isabelle Petit-Härtlein , Cécile Breyton , Aline Le Roy , Michel Thépaut , et al.
Biophysical Journal, 2020, 119 (3), pp.605-618. ⟨10.1016/j.bpj.2020.06.025⟩
Article dans une revue hal-02921448v1
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HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions

Georgy Derevyanko , Sergei Grudinin
Acta crystallographica Section D : Structural biology [1993-..], 2014, 70 (8), pp.2069-2084. ⟨10.1107/S1399004714011493⟩
Article dans une revue istex hal-01078550v1

Predicting Binding Poses and Affinities in the CSAR 2013―2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential

Sergei Grudinin , Petr Popov , Emilie Neveu , Georgy Cheremovskiy
Journal of Chemical Information and Modeling, 2016, 56 (6), pp.1053-1062. ⟨10.1021/acs.jcim.5b00339⟩
Article dans une revue hal-01258022v1
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6DCNN with roto-translational convolution filters for volumetric data processing

Dmitrii Zhemchuzhnikov , Ilia Igashov , Sergei Grudinin
The Thirty-Sixth AAAI Conference on Artificial Intelligence (AAAI-22), AAAI, Feb 2022, Vancouver, Canada. pp.4707-4715
Communication dans un congrès hal-03298699v2
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A novel fast Fourier transform accelerated off-grid exhaustive search method for cryo-electron microscopy fitting

Alexandre Hoffmann , Valérie Perrier , Sergei Grudinin
Journal of Applied Crystallography, 2017, 50 (4), pp.1036-1047. ⟨10.1107/S1600576717008172⟩
Article dans une revue hal-01553293v1

Principal component analysis of lipid molecule conformational changes in molecular dynamics simulations

Pavel Buslaev , Valentin I. Gordeliy , Sergei Grudinin , Ivan Yu. Gushchin
Journal of Chemical Theory and Computation, 2016, 12 (3), pp.1019-1028. ⟨10.1021/acs.jctc.5b01106⟩
Article dans une revue hal-01258167v1