Protein–ligand docking using FFT based sampling: D3R case study

Autor: Dzmitry Padhorny, Mohammad Moghadasi, David R. Hall, Hanieh Mirzaei, Andrey Alekseenko, Dmitri Beglov, Artem B. Mamonov, Dima Kozakov

Publikováno v: Journal of Computer-Aided Molecular Design. 32:225-230

Fast Fourier Transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein-protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein-peptide interaction

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::390077082b8ab2891a0158cd753663d3
https://doi.org/10.1007/s10822-017-0069-7

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro

Autor: Artem B. Mamonov, Dima Kozakov, Sandor Vajda, Seppe Leysen, Sergei V. Strelkov, Bing Xia, Ioannis Ch. Paschalidis, Karen N. Allen

Publikováno v: Journal of Computational Chemistry. 36:1568-1572

The protein-protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near-native ones for many proteins,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d80f3364f92431ac068ba11152ab4f26
https://doi.org/10.1002/jcc.23952

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

Autor: Eichiro Ichiishi, Dmitri Beglov, Bernard Maigret, Gyu Rie Lee, Artem B. Mamonov, Shoshana J. Wodak, Jonathan C. Fuller, Dima Kozakov, Jong Young Joung, Petr Popov, Xiaofeng Yu, Keehyoung Joo, João P. G. L. M. Rodrigues, Anna Vangone, Koen M. Visscher, Xiaoqin Zou, Paul A. Bates, Andriy Kryshtafovych, Shourya S. Roy Burman, Daisuke Kihara, Romina Oliva, Efrat Ben-Zeev, Jeffrey J. Gray, Yang Shen, Li C. Xue, Sameer Velankar, Emilie Neveu, Shruthi Viswanath, Dina Schneidman-Duhovny, Juan Esquivel-Rodríguez, Mieczyslaw Torchala, Amit Roy, Alexandre M. J. J. Bonvin, David R. Hall, Tanggis Bohnuud, Xusi Han, David W. Ritchie, Ron Elber, Daisuke Kuroda, Zhiwei Ma, Joan Segura, Carlos A. Del Carpio, Nicholas A. Marze, Jong Yun Kim, Andrej Sali, Petras J. Kundrotas, Ezgi Karaca, Neil J. Bruce, Chaok Seok, Panagiotis L. Kastritis, Shen You Huang, Ilya A. Vakser, Lim Heo, Sanbo Qin, Raphael A. G. Chaleil, Adrien S. J. Melquiond, Miguel Romero-Durana, Anisah W. Ghoorah, Surendra S. Negi, Andrey Tovchigrechko, Françoise Ochsenbein, Narcis Fernandez-Fuentes, Liming Qiu, Miriam Eisenstein, Mehdi Nellen, Marie-Dominique Devignes, Lenna X. Peterson, Jinchao Yu, Minkyung Baek, Brian G. Pierce, Hasup Lee, Toshiyuki Oda, Rebecca C. Wade, Raphael Guerois, Juan Fernández-Recio, Iain H. Moal, Edrisse Chermak, Sergei Grudinin, Sangwoo Park, Ivan Anishchenko, Chengfei Yan, Thom Vreven, Kentaro Tomii, Bing Xia, Hyung Rae Kim, Chiara Pallara, Jooyoung Lee, Kazunori D. Yamada, Xianjin Xu, Kenichiro Imai, Zhiping Weng, Luigi Cavallo, Tyler M. Borrman, Jianlin Cheng, Marc F. Lensink, Huan-Xiang Zhou, Jilong Li, Gydo C. P. van Zundert, Brian Jiménez-García, Tsukasa Nakamura, Scott E. Mottarella, Sandor Vajda

Publikováno v: Proteins-Structure, Function and Bioinformatics
Proteins-Structure, Function and Bioinformatics, Wiley, 2016, Special Issue: Eleventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, 84 (S1), pp.323-348 〈10.1002/prot.25007〉
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⟩
Proteins-Structure, Function and Bioinformatics, Wiley, 2016, Special Issue: Eleventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, 84 (S1), pp.323-348. ⟨10.1002/prot.25007⟩
Recercat. Dipósit de la Recerca de Catalunya
instname
Proteins
Proteins: Structure function and bioinformatics, 84(S1), 323. Wiley-Liss Inc.
UPCommons. Portal del coneixement obert de la UPC
Universitat Politècnica de Catalunya (UPC)

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets from amongst those submit

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8102faf768692c2ecf1ed7b49988fca7
https://hal.inria.fr/hal-01309105

Absolute free energies estimated by combining precalculated molecular fragment libraries

Autor: Artem B. Mamonov, Xin Zhang, Daniel M. Zuckerman

Publikováno v: Journal of Computational Chemistry. 30:1680-1691

The absolute free energy — or partition function, equivalently — of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule based o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::664ce03d13c979de3628cd05d27a3826
https://doi.org/10.1002/jcc.21337

The impact of side-chain packing on protein docking refinement

Autor: Hanieh Mirzaei, Ioannis Ch. Paschalidis, Sandor Vajda, Artem B. Mamonov, Dima Kozakov, Mohammad Moghadasi, Pirooz Vakili

Publikováno v: Journal of chemical information and modeling. 55(4)

We study the impact of optimizing the side-chain positions in the interface region between two proteins during the process of binding. Mathematically, the problem is similar to side-chain prediction, which has been extensively explored in the process

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::69f7bf9c8c6d4fc0ea3af6ef537c0c4a
https://pubmed.ncbi.nlm.nih.gov/25714358