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Year Number of Results
2016 2
2017 2
2018 1
2019 2
2020 3
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Page 1
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ. Lensink MF, et al. Among authors: kadukova m. Proteins. 2019 Dec;87(12):1200-1221. doi: 10.1002/prot.25838. Epub 2019 Oct 25. Proteins. 2019. PMID: 31612567
Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4.
Kadukova M, Chupin V, Grudinin S. Kadukova M, et al. J Comput Aided Mol Des. 2020 Feb;34(2):191-200. doi: 10.1007/s10822-019-00263-3. Epub 2019 Nov 29. J Comput Aided Mol Des. 2020. PMID: 31784861
Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization.
Kadukova M, Grudinin S. Kadukova M, et al. J Comput Aided Mol Des. 2017 Oct;31(10):943-958. doi: 10.1007/s10822-017-0068-8. Epub 2017 Sep 18. J Comput Aided Mol Des. 2017. PMID: 28921375
Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2.
Kadukova M, Grudinin S. Kadukova M, et al. J Comput Aided Mol Des. 2018 Jan;32(1):151-162. doi: 10.1007/s10822-017-0062-1. Epub 2017 Sep 14. J Comput Aided Mol Des. 2018. PMID: 28913782
KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions.
Kadukova M, Machado KDS, Chacón P, Grudinin S. Kadukova M, et al. Bioinformatics. 2020 Aug 25:btaa748. doi: 10.1093/bioinformatics/btaa748. Online ahead of print. Bioinformatics. 2020. PMID: 32840574
Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450.
Bukhdruker S, Varaksa T, Grabovec I, Marin E, Shabunya P, Kadukova M, Grudinin S, Kavaleuski A, Gusach A, Gilep A, Borshchevskiy V, Strushkevich N. Bukhdruker S, et al. Among authors: kadukova m. Int J Mol Sci. 2020 Oct 16;21(20):7683. doi: 10.3390/ijms21207683. Int J Mol Sci. 2020. PMID: 33081390 Free PMC 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.
Grudinin S, Kadukova M, Eisenbarth A, Marillet S, Cazals F. Grudinin S, et al. Among authors: kadukova m. J Comput Aided Mol Des. 2016 Sep;30(9):791-804. doi: 10.1007/s10822-016-9976-2. Epub 2016 Oct 7. J Comput Aided Mol Des. 2016. PMID: 27718029
Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates.
Kadukova M, Grudinin S. Kadukova M, et al. J Chem Inf Model. 2016 Aug 22;56(8):1410-9. doi: 10.1021/acs.jcim.5b00512. Epub 2016 Jul 21. J Chem Inf Model. 2016. PMID: 27405533
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