Sergei Grudinin

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 19

Top Topics

Molecular Dynamics Simulations

Machine Learning

Protein Protein

Top Venues

Scientific data

Journal of computer-aided molecular design

Proceedings of the National Academy of Sciences of the United States of America

This page only lists publications with an associated author ORCID identifier.

Publications

Harold W Hatch, Christina Bergonzo, Marco A Blanco, Guangcui Yuan, Sergei Grudinin, Mikael Lund, Joseph E Curtis, Alexander V Grishaev, Yun Liu, Vincent K Shen
Anisotropic coarse-grain Monte Carlo simulations of lysozyme, lactoferrin, and NISTmAb by precomputing atomistic models. The Journal of chemical physics 161 (9) (2024)
Valentin Lombard, Sergei Grudinin, Elodie Laine
Explaining Conformational Diversity in Protein Families through Molecular Motions. Scientific data 11 (1) (2024)
Valentin Lombard, Sergei Grudinin, Elodie Laine
Explaining Conformational Diversity in Protein Families through Molecular Motions. Scientific data 11 (1) (2024)
Valentin Lombard, Sergei Grudinin, Elodie Laine
Explaining Conformational Diversity in Protein Families through Molecular Motions. Scientific data 11 (1) (2024)
Sri Devan Appasamy, John Berrisford, Romana Gaborova, Sreenath Nair, Stephen Anyango, Sergei Grudinin, Mandar Deshpande, David Armstrong, Ivanna Pidruchna, Joseph I J Ellaway, Grisell Díaz Leines, Deepti Gupta, Deborah Harrus, Mihaly Varadi, Sameer Velankar
Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. Scientific data 10 (1) (2023)
Ilya A Vakser, Sergei Grudinin, Nathan W Jenkins, Petras J Kundrotas, Eric J Deeds
Docking-based long timescale simulation of cell-size protein systems at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America 119 (41) (2022)
Elodie Laine, Sergei Grudinin
HOPMA: Boosting Protein Functional Dynamics with Colored Contact Maps. The journal of physical chemistry. B 125 (10) (2021)
Elodie Laine, Stephan Eismann, Arne Elofsson, Sergei Grudinin
Protein sequence-to-structure learning: Is this the end(-to-end revolution)? Proteins 89 (12) (2021)
Marc F Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael A G Chaleil, Tereza Clarence, Paul A Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Agnieszka G Lipska, Adam Liwo, Emilia A Lubecka, Martyna Maszota-Zieleniak, Adam K Sieradzan, Rafał Ślusarz, Patryk A Wesołowski, Karolina Zięba, Carlos A Del Carpio Muñoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J Gray, Alexandre M J J Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jiménez-García, Panagiotis I Koukos, Siri Van Keulen, Charlotte W Van Noort, Manon Réau, Jorge Roel-Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A Rodríguez-Lumbreras, Juan Fernández-Recio, Agnieszka Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng-You Huang, Charles W Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G 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 J Kundrotas, Amar Singh, Ilya A Vakser, Justas Dapkunas, Kliment Olechnovič, Česlovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J Wodak
Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins 89 (12) (2021)
Maria Kadukova, Karina Dos Santos Machado, Pablo Chacón, Sergei Grudinin
KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions. Bioinformatics (Oxford, England) 37 (7) (2021)
Andreas Haahr Larsen, Yong Wang, Sandro Bottaro, Sergei Grudinin, Lise Arleth, Kresten Lindorff-Larsen
Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution. PLoS computational biology 16 (4) (2020)
Maria Kadukova, Vladimir Chupin, Sergei Grudinin
Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4. Journal of computer-aided molecular design 34 (2) (2019)
Petr A Popov, Sergei Grudinin, Andrii Kurdiuk, Pavel Buslaev, Stephane Redon
Controlled-advancement rigid-body optimization of nanosystems. Journal of computational chemistry 40 (27) (2019)
Greg L Hura, Curtis D Hodge, Daniel Rosenberg, Dmytro Guzenko, Jose M Duarte, Bohdan Monastyrskyy, Sergei Grudinin, Andriy Kryshtafovych, John A Tainer, Krzysztof Fidelis, Susan E Tsutakawa
Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences. Proteins 87 (12) (2019)
Maria Kadukova, Sergei Grudinin
Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2. Journal of computer-aided molecular design 32 (1) (2017)
Maria Kadukova, Sergei Grudinin
Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization. Journal of computer-aided molecular design 31 (10) (2017)
Alexandre Hoffmann, Sergei Grudinin
NOLB: Nonlinear Rigid Block Normal-Mode Analysis Method. Journal of chemical theory and computation 13 (5) (2017)
Ivan Yu Gushchin, Igor Melnikov, Vitaly Polovinkin, Andrii Ishchenko, Anastasia Yuzhakova, Pavel Buslaev, Gleb Bourenkov, Sergei Grudinin, Ekaterina Round, Taras Balandin, Valentin I Borshchevskiy, Dieter Willbold, Gordon A Leonard, Georg Büldt, Alexander N Popov, Valentin I Gordeliy
Mechanism of transmembrane signaling by sensor histidine kinases. Science (New York, N.Y.) 356 (6342) (2017)
Sergei Grudinin, Maria Kadukova, Andreas Eisenbarth, Simon Marillet, Frédéric Cazals
Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation. Journal of computer-aided molecular design 30 (9) (2016)