Works by Grudinin, Sergei

Results: 36

A novel fast Fourier transform accelerated off-grid exhaustive search method for cryo-electron microscopy fitting.

Published in:

Journal of Applied Crystallography, 2017, v. 50, n. 4, p. 1036, doi. 10.1107/S1600576717008172

By:

Hoffmann, Alexandre;
Perrier, Valérie;
Grudinin, Sergei

Publication type:

Article

Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry.

Published in:

Journal of Applied Crystallography, 2016, v. 49, n. 1, p. 158, doi. 10.1107/S1600576715022931

By:

Ritchie, David W.;
Grudinin, Sergei

Publication type:

Article

Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4.

Published in:

Journal of Computer-Aided Molecular Design, 2020, v. 34, n. 2, p. 191, doi. 10.1007/s10822-019-00263-3

By:

Kadukova, Maria;
Chupin, Vladimir;
Grudinin, Sergei

Publication type:

Article

Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 151, doi. 10.1007/s10822-017-0062-1

By:

Kadukova, Maria;
Grudinin, Sergei

Publication type:

Article

Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization.

Published in:

Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 10, p. 943, doi. 10.1007/s10822-017-0068-8

By:

Kadukova, Maria;
Grudinin, Sergei

Publication type:

Article

Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation.

Published in:

Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 9, p. 791, doi. 10.1007/s10822-016-9976-2

By:

Grudinin, Sergei;
Kadukova, Maria;
Eisenbarth, Andreas;
Marillet, Simon;
Cazals, Frédéric

Publication type:

Article

Explaining Conformational Diversity in Protein Families through Molecular Motions.

Published in:

Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03524-5

By:

Lombard, Valentin;
Grudinin, Sergei;
Laine, Elodie

Publication type:

Article

Explaining Conformational Diversity in Protein Families through Molecular Motions.

Published in:

Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03524-5

By:

Lombard, Valentin;
Grudinin, Sergei;
Laine, Elodie

Publication type:

Article

Controlled‐advancement rigid‐body optimization of nanosystems.

Published in:

Journal of Computational Chemistry, 2019, v. 40, n. 27, p. 2391, doi. 10.1002/jcc.26016

By:

Popov, Petr;
Grudinin, Sergei;
Kurdiuk, Andrii;
Buslaev, Pavel;
Redon, Stephane

Publication type:

Article

Rapid determination of RMSDs corresponding to macromolecular rigid body motions.

Published in:

Journal of Computational Chemistry, 2014, v. 35, n. 12, p. 950, doi. 10.1002/jcc.23569

By:

Popov, Petr;
Grudinin, Sergei

Publication type:

Article

Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450.

Published in:

International Journal of Molecular Sciences, 2020, v. 21, n. 20, p. 7683, doi. 10.3390/ijms21207683

By:

Bukhdruker, Sergey;
Varaksa, Tatsiana;
Grabovec, Irina;
Marin, Egor;
Shabunya, Polina;
Kadukova, Maria;
Grudinin, Sergei;
Kavaleuski, Anton;
Gusach, Anastasiia;
Gilep, Andrei;
Borshchevskiy, Valentin;
Strushkevich, Natallia

Publication type:

Article

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution.

Published in:

PLoS Computational Biology, 2020, v. 16, n. 4, p. 1, doi. 10.1371/journal.pcbi.1007870

By:

Larsen, Andreas Haahr;
Wang, Yong;
Bottaro, Sandro;
Grudinin, Sergei;
Arleth, Lise;
Lindorff-Larsen, Kresten

Publication type:

Article

VoroCNN: deep convolutional neural network built on 3D Voronoi tessellation of protein structures.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2332, doi. 10.1093/bioinformatics/btab118

By:

Igashov, Ilia;
Olechnovič, Kliment;
Kadukova, Maria;
Venclovas, Česlovas;
Grudinin, Sergei

Publication type:

Article

KORP-PL: a coarse-grained knowledge-based scoring function for protein–ligand interactions.

Published in:

Bioinformatics, 2021, v. 37, n. 7, p. 943, doi. 10.1093/bioinformatics/btaa748

By:

Kadukova, Maria;
Machado, Karina dos Santos;
Chacón, Pablo;
Grudinin, Sergei

Publication type:

Article

DeepSymmetry: using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5113, doi. 10.1093/bioinformatics/btz454

By:

Pagès, Guillaume;
Grudinin, Sergei

Publication type:

Article

Protein model quality assessment using 3D oriented convolutional neural networks.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3313, doi. 10.1093/bioinformatics/btz122

By:

Pagès, Guillaume;
Charmettant, Benoit;
Grudinin, Sergei

Publication type:

Article

Smooth orientation-dependent scoring function for coarse-grained protein quality assessment.

Published in:

Bioinformatics, 2019, v. 35, n. 16, p. 2801, doi. 10.1093/bioinformatics/bty1037

By:

Karasikov, Mikhail;
Pagès, Guillaume;
Grudinin, Sergei

Publication type:

Article

Deep convolutional networks for quality assessment of protein folds.

Published in:

Bioinformatics, 2018, v. 34, n. 23, p. 4046, doi. 10.1093/bioinformatics/bty494

By:

Derevyanko, Georgy;
Grudinin, Sergei;
Bengio, Yoshua;
Lamoureux, Guillaume

Publication type:

Article

PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. i693, doi. 10.1093/bioinformatics/btw443

By:

Neveu, Emilie;
Ritchie, David W.;
Popov, Petr;
Grudinin, Sergei

Publication type:

Article

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

Published in:

Nature Communications, 2014, v. 5, n. 6, p. 4169, doi. 10.1038/ncomms5169

By:

Nogly, Przemyslaw;
Gushchin, Ivan;
Remeeva, Alina;
Esteves, Ana M.;
Borges, Nuno;
Ma, Pikyee;
Ishchenko, Andrii;
Grudinin, Sergei;
Round, Ekaterina;
Moraes, Isabel;
Borshchevskiy, Valentin;
Santos, Helena;
Gordeliy, Valentin;
Archer, Margarida

Publication type:

Article

Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles.

Published in:

Acta Crystallographica: Section D, Structural Biology, 2017, v. 73, n. 5, p. 449, doi. 10.1107/S2059798317005745

By:

Grudinin, Sergei;
Garkavenko, Maria;
Kazennov, Andrei

Publication type:

Article

Two Distinct States of the HAMP Domain from Sensory Rhodopsin Transducer Observed in Unbiased Molecular Dynamics Simulations.

Published in:

PLoS ONE, 2013, v. 8, n. 7, p. 1, doi. 10.1371/journal.pone.0066917

By:

Gushchin, Ivan;
Gordeliy, Valentin;
Grudinin, Sergei

Publication type:

Article

Block-adaptive quantum mechanics: An adaptive divide-and-conquer approach to interactive quantum chemistry.

Published in:

Journal of Computational Chemistry, 2013, v. 34, n. 6, p. 492, doi. 10.1002/jcc.23157

By:

Bosson, Maël;
Grudinin, Sergei;
Redon, Stephane

Publication type:

Article

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

Published in:

Journal of Computational Chemistry, 2012, v. 33, n. 7, p. 779, doi. 10.1002/jcc.22905

By:

Bosson, Mäel;
Richard, Caroline;
Plet, Antoine;
Grudinin, Sergei;
Redon, Stephane

Publication type:

Article

A comparison of neighbor search algorithms for large rigid molecules.

Published in:

Journal of Computational Chemistry, 2011, v. 32, n. 13, p. 2865, doi. 10.1002/jcc.21868

By:

Artemova, Svetlana;
Grudinin, Sergei;
Redon, Stephane

Publication type:

Article

Fast construction of assembly trees for molecular graphs.

Published in:

Journal of Computational Chemistry, 2011, v. 32, n. 8, p. 1589, doi. 10.1002/jcc.21738

By:

Artemova, Svetlana;
Grudinin, Sergei;
Redon, Stephane

Publication type:

Article

Practical modeling of molecular systems with symmetries.

Published in:

Journal of Computational Chemistry, 2010, v. 31, n. 9, p. 1799, doi. 10.1002/jcc.21434

By:

GRUDININ, SERGEI;
REDON, STEPHANE

Publication type:

Article

Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13.

Published in:

2020

By:

Fajardo, J. Eduardo;
Shrestha, Rojan;
Gil, Nelson;
Belsom, Adam;
Crivelli, Silvia N.;
Czaplewski, Cezary;
Fidelis, Krzysztof;
Grudinin, Sergei;
Karasikov, Mikhail;
Karczyńska, Agnieszka S.;
Kryshtafovych, Andriy;
Leitner, Alexander;
Liwo, Adam;
Lubecka, Emilia A.;
Monastyrskyy, Bohdan;
Pagès, Guillaume;
Rappsilber, Juri;
Sieradzan, Adam K.;
Sikorska, Celina;
Trabjerg, Esben

Publication type:

Correction Notice

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment.

Published in:

Proteins, 2019, v. 87, n. 12, p. 1200, doi. 10.1002/prot.25838

By:

Lensink, Marc F.;
Brysbaert, Guillaume;
Nadzirin, Nurul;
Velankar, Sameer;
Chaleil, Raphaël A. G.;
Gerguri, Tereza;
Bates, Paul A.;
Laine, Elodie;
Carbone, Alessandra;
Grudinin, Sergei;
Kong, Ren;
Liu, Ran‐Ran;
Xu, Xi‐Ming;
Shi, Hang;
Chang, Shan;
Eisenstein, Miriam;
Karczynska, Agnieszka;
Czaplewski, Cezary;
Lubecka, Emilia;
Lipska, Agnieszka

Publication type:

Article

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

Published in:

Proteins, 2019, v. 87, n. 12, p. 1298, doi. 10.1002/prot.25827

By:

Hura, Greg L.;
Hodge, Curtis D.;
Rosenberg, Daniel;
Guzenko, Dmytro;
Duarte, Jose M.;
Monastyrskyy, Bohdan;
Grudinin, Sergei;
Kryshtafovych, Andriy;
Tainer, John A.;
Fidelis, Krzysztof;
Tsutakawa, Susan E.

Publication type:

Article

Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13.

Published in:

Proteins, 2019, v. 87, n. 12, p. 1283, doi. 10.1002/prot.25816

By:

Fajardo, J. Eduardo;
Shrestha, Rojan;
Gil, Nelson;
Belsom, Adam;
Crivelli, Silvia N.;
Czaplewski, Cezary;
Fidelis, Krzysztof;
Grudinin, Sergei;
Karasikov, Mikhail;
Karczyńska, Agnieszka S.;
Kryshtafovych, Andriy;
Leitner, Alexander;
Liwo, Adam;
Lubecka, Emilia A.;
Monastyrskyy, Bohdan;
Pagès, Guillaume;
Rappsilber, Juri;
Sieradzan, Adam K.;
Sikorska, Celina;
Trabjerg, Esben

Publication type:

Article

Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models.

Published in:

Proteins, 2017, v. 85, n. 3, p. 463, doi. 10.1002/prot.25182

By:

El Houasli, Marwa;
Maigret, Bernard;
Devignes, Marie‐Dominique;
Ghoorah, Anisah W.;
Grudinin, Sergei;
Ritchie, David W.

Publication type:

Article

Prediction of homoprotein and heteroprotein complexes by protein docking and templatebased modeling: A CASP-CAPRI experiment.

Published in:

Proteins, 2016, v. 84, p. 323, doi. 10.1002/prot.25007

By:

Lensink, Marc F.;
Velankar, Sameer;
Kryshtafovych, Andriy;
Huang, Shen‐You;
Schneidman‐Duhovny, Dina;
Sali, Andrej;
Segura, Joan;
Fernandez‐Fuentes, Narcis;
Viswanath, Shruthi;
Elber, Ron;
Grudinin, Sergei;
Popov, Petr;
Neveu, Emilie;
Lee, Hasup;
Baek, Minkyung;
Park, Sangwoo;
Heo, Lim;
Rie Lee, Gyu;
Seok, Chaok;
Qin, Sanbo

Publication type:

Article

DockTrina: Docking triangular protein trimers.

Published in:

Proteins, 2014, v. 82, n. 1, p. 34, doi. 10.1002/prot.24344

By:

Popov, Petr;
Ritchie, David W.;
Grudinin, Sergei

Publication type:

Article

A novel dimerization interface of cyclic nucleotide binding domain, which is disrupted in presence of cAMP: implications for CNG channels gating.

Published in:

Journal of Molecular Modeling, 2012, v. 18, n. 9, p. 4053, doi. 10.1007/s00894-012-1404-5

By:

Gushchin, Ivan;
Gordeliy, Valentin;
Grudinin, Sergei

Publication type:

Article

Protein sequence‐to‐structure learning: Is this the end(‐to‐end revolution)?

Published in:

Proteins, 2021, v. 89, n. 12, p. 1770, doi. 10.1002/prot.26235

By:

Laine, Elodie;
Eismann, Stephan;
Elofsson, Arne;
Grudinin, Sergei

Publication type:

Article