VESPER: global and local cryo-EM map alignment using local density vectors

Autor: Xusi Han, Genki Terashi, Charles Christoffer, Siyang Chen, Daisuke Kihara

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)

Here, the authors present VESPER, a program for EM density map search and alignment. Using benchmark datasets, they demonstrate that VESPER performs accurate global and local alignments and comparisons of EM maps.

Externí odkaz: https://doaj.org/article/80c1de7ec4114f6c9d64b4218118b846

VESPER: global and local cryo-EM map alignment using local density vectors

Autor: Siyang Chen, Daisuke Kihara, Xusi Han, Charles Christoffer, Genki Terashi

Publikováno v: Nature Communications
Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)

An increasing number of density maps of biological macromolecules have been determined by cryo-electron microscopy (cryo-EM) and stored in the public database, EMDB. To interpret the structural information contained in EM density maps, alignment of m

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2141f7631e4ed393a66a7f77bc13f18d
https://doi.org/10.1038/s41467-021-22401-y

Protein Shape Retrieval Contest

Autor: Florent, Langenfeld, Apostolos, Axenopoulos, Halim, Benhabiles, Petros, Daras, Giachetti, Andrea, Xusi, Han, Karim, Hammoudi, Daisuke, Kihara, Lai, Tuan M., Haiguang, Liu, Mahmoud, Melkemi, Mylonas, Stelios K., Genki, Terashi, Yufan, Wang, Feryal, Windal, Matthieu, Montes

This track aimed at retrieving protein evolutionary classification based on their surfaces meshes only. Given that proteins are dynamic, non-rigid objects and that evolution tends to conserve patterns related to their activity and function, this trac

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::94cbf0a44255309c8dcc4a01144a05a6

Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER

Autor: Daisuke Kihara, Qing Wei, Xusi Han

Publikováno v: Current protocols in bioinformatics. 60

With the rapid growth in the number of solved protein structures stored in the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB), it is essential to develop tools to perform real-time structure similarity searches against the entir

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0f7b34d0c2c9e5fb4c2fb6fcbd6233c7
https://pubmed.ncbi.nlm.nih.gov/29220075

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