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authIdHal_s : sergei-grudinin
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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⟩
Journal articles hal-01591154v1
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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⟩
Book sections hal-02931690v1

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⟩
Journal articles hal-02931707v1

Controlled‐advancement rigid‐body optimization of nanosystems

Petr Popov , Sergei Grudinin , Andrii Kurdiuk , Pavel Buslaev , Stephane Redon et al.
Journal of Computational Chemistry, 2019, 40 (27), pp.2391-2399. ⟨10.1002/jcc.26016⟩
Journal articles hal-02315276v1
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User Guide for AnAnaS : Analytical Analyzer of Symmetries

Guillaume Pagès , Sergei Grudinin
Preprints, Working Papers, ... hal-01644987v1
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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⟩
Journal articles hal-02931666v1
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Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2

Maria Kadukova , Sergei Grudinin
Journal of Computer-Aided Molecular Design, 2018, 32 (1), pp.151-162. ⟨10.1007/s10822-017-0062-1⟩
Journal articles hal-01591157v1
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Eurecon: Equidistant Uniform Rigid-body Ensemble Constructor

Petr Popov , Sergei Grudinin
Journal of Molecular Graphics and Modelling, 2018, 80, pp.313-319. ⟨10.1016/j.jmgm.2018.01.015⟩
Journal articles hal-01702810v1
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Inverse Protein Folding Problem via Quadratic Programming

Andrii Riazanov , Mikhail Karasikov , Sergei Grudinin
Information Technology and Systems 2016, Sep 2016, Repino, St. Petersburg, Russia. pp.561-568
Conference papers hal-01419374v2
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Quadratic Programming Approach to Fit Protein Complexes into Electron Density Maps

Roman Pogodin , Alexander Katrutsa , Sergei Grudinin
Information Technology and Systems 2016, Sep 2016, Repino, St. Petersburg, Russia. pp.576-582
Conference papers hal-01419380v2
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DeepSymmetry : Using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures

Guillaume Pagès , Sergei Grudinin
Bioinformatics, 2019, 35 (24), pp.5113-5120. ⟨10.1093/bioinformatics/btz454⟩
Journal articles hal-01903624v1
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VoroCNN: Deep convolutional neural network built on 3D Voronoi tessellation of protein structures

Ilia Igashov , Kliment Olechnovic , Maria Kadukova , Česlovas Venclovas , Sergei Grudinin et al.
Bioinformatics, 2021, 37 (16), pp.2332-2339. ⟨10.1093/bioinformatics/btab118⟩
Journal articles hal-02558004v1

3D live cell imaging of whole organoids in time-lapse using intensity diffraction tomography

William Pierré , Lionel Hervé , Cédric Allier , Sophie Morales , Sergei Grudinin et al.
SPIE Photonics Europe, Apr 2022, Strasbourg, France. ⟨10.1117/12.2625734⟩
Conference papers hal-03874785v1
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NOLB: Nonlinear Rigid Block Normal Mode Analysis Method

Alexandre Hoffmann , Sergei Grudinin
Journal of Chemical Theory and Computation, 2017, 13 (5), pp.2123-2134. ⟨10.1021/acs.jctc.7b00197⟩
Journal articles hal-01505843v2
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Convex-PL-R - Revisiting affinity predictions and virtual screening using physics-informed machine learning

Maria Kadukova , Vladimir Chupin , Sergei Grudinin
Preprints, Working Papers, ... hal-03342508v1

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Rocco Moretti , Sarel J Fleishman , Rudi Agius , Mieczyslaw Torchala , Paul A. Bates et al.
Proteins - Structure, Function and Bioinformatics, 2013, 81 (11), pp.1980 - 1987. ⟨10.1002/prot.24356⟩
Journal articles hal-00905794v1

X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism

Przemyslaw Nogly , Ivan Yu. Gushchin , Alina Remeeva , Ana M. Esteves , Nuno Borges et al.
Nature Communications, 2014, 5, pp.Article number: 4169. ⟨10.1038/ncomms5169⟩
Journal articles hal-01018657v1

Practical modeling of molecular systems with symmetries

Sergei Grudinin , Stephane Redon
Journal of Computational Chemistry, 2010, 31 (9), pp.1799-1814. ⟨10.1002/jcc.21434⟩
Journal articles istex hal-00748028v1

A comparison of neighbor search algorithms for large rigid molecules

Svetlana Artemova , Sergei Grudinin , Stephane Redon
Journal of Computational Chemistry, 2011, 32 (13), pp.2865-2877. ⟨10.1002/jcc.21868⟩
Journal articles istex hal-00748053v1
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Analytical symmetry detection in protein assemblies. I. Cyclic symmetries

Guillaume Pagès , Elvira Kinzina , Sergei Grudinin
Journal of Structural Biology, 2018, 203 (2), pp.142-148. ⟨10.1016/j.jsb.2018.04.004⟩
Journal articles hal-01779893v1
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Role of the HAMP Domain Region of Sensory Rhodopsin Transducers in Signal Transduction

Ivan Yu. Gushchin , Valentin I. Gordeliy , Sergei Grudinin
Biochemistry, 2010, 50 (4), pp.574-580. ⟨10.1021/bi101032a⟩
Journal articles hal-00784550v1

Deep convolutional networks for quality assessment of protein folds

Georgy Derevyanko , Sergei Grudinin , Yoshua Bengio , Guillaume Lamoureux
Bioinformatics, 2018, 34 (23), pp.4046-4053. ⟨10.1093/bioinformatics/bty494⟩
Journal articles hal-01702857v1
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RapidRMSD: Rapid determination of RMSDs corresponding to motions of flexible molecules

Emilie Neveu , Petr Popov , Alexandre Hoffmann , Angelo Migliosi , Xavier Besseron et al.
Bioinformatics, 2018, 34 (16), pp.2757-2765. ⟨10.1093/bioinformatics/bty160⟩
Journal articles hal-01735214v1
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment

Andriy Kryshtafovych , John Moult , Wendy M Billings , Dennis Della Corte , Krzysztof Fidelis et al.
Proteins - Structure, Function and Bioinformatics, 2021, 89 (12), pp.1987-1996. ⟨10.1002/prot.26231⟩
Journal articles hal-03454382v1
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Predicting binding poses and affinities for protein-ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation

Sergei Grudinin , Maria Kadukova , Andreas Eisenbarth , Simon Marillet , Frédéric Cazals et al.
Journal of Computer-Aided Molecular Design, 2016, 30 (9), pp.791-804. ⟨10.1007/s10822-016-9976-2⟩
Journal articles hal-01377738v1

Deep learning framework applied to optical diffraction tomography (ODT)

William Pierré , Lionel Hervé , Cédric Allier , Sophie Morales , Sergei Grudinin et al.
Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVIII, SPIE, Mar 2021, Online Only, France. pp.1, ⟨10.1117/12.2582361⟩
Conference papers hal-03454249v1

Block-Adaptive Quantum Mechanics: An Adaptive Divide-and-Conquer Approach to Interactive Quantum Chemistry

Maël Bosson , Sergei Grudinin , Stephane Redon
Journal of Computational Chemistry, 2013, 34 (6), pp.492-504. ⟨10.1002/jcc.23157⟩
Journal articles istex hal-00755521v1

Interactive quantum chemistry: A divide-and-conquer ASED-MO method

Maël Bosson , Antoine Plet , Sergei Grudinin , Stephane Redon , Caroline Richard et al.
Journal of Computational Chemistry, 2012, 33 (7), pp.779-790. ⟨10.1002/jcc.22905⟩
Journal articles istex hal-00755498v1
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Active State of Sensory Rhodopsin II: Structural determinants for signal transfer and proton pumping

Ivan Yu. Gushchin , Anastasia Reshetnyak , Valentin Borshchevskiy , Andrii Ishchenko , Ekaterina Round et al.
Journal of Molecular Biology, 2011, 412 (4), pp.591-600. ⟨10.1016/j.jmb.2011.07.022⟩
Journal articles hal-00766090v1

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Marc F. Lensink , Sameer Velankar , Andriy Kryshtafovych , Shen-You Huang , Dina Schneidman-Duhovy et al.
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⟩
Journal articles hal-01309105v1