Modeling disordered protein interactions from biophysical principles.

Autor: Lenna X Peterson, Amitava Roy, Charles Christoffer, Genki Terashi, Daisuke Kihara

Publikováno v: PLoS Computational Biology, Vol 13, Iss 4, p e1005485 (2017)

Disordered protein-protein interactions (PPIs), those involving a folded protein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important signaling and regulatory pathways. IDPs do not adopt a single dominant stru

Externí odkaz: https://doaj.org/article/3cf5f1d94cc04c2db175e95c3f04636f

Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38-46

Autor: Charles Christoffer, Daisuke Kihara, Jacob Verburgt, Lenna X. Peterson, Woong-Hee Shin, Genki Terashi, Sai Raghavendra Maddhuri Venkata Subramaniya, Tunde Aderinwale

Publikováno v: Proteins

We report the performance of the protein docking prediction pipeline of our group and the results for Critical Assessment of Prediction of Interactions (CAPRI) rounds 38-46. The pipeline integrates programs developed in our group as well as other exi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1e4b2b152e18a6ee81458f7acd2911d3
https://pubmed.ncbi.nlm.nih.gov/31697428

Modeling the assembly order of multimeric heteroprotein complexes

Autor: Genki Terashi, Juan Esquivel-Rodríguez, Lenna X. Peterson, A. Roy, Woong-Hee Shin, Charles Christoffer, Yoichiro Togawa, Daisuke Kihara

Publikováno v: PLoS Computational Biology, Vol 14, Iss 1, p e1005937 (2018)
PLoS Computational Biology

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6fec7e9120d339e3f346ebc11b125736
http://europepmc.org/articles/PMC5785014?pdf=render

Assessment of protein side-chain conformation prediction methods in different residue environments

Autor: Xuejiao Kang, Lenna X. Peterson, Daisuke Kihara

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 82:1971-1984

Computational prediction of side-chain conformation is an important component of protein structure prediction. Accurate side-chain prediction is crucial for practical applications of protein structure models that need atomic-detailed resolution such

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::942bc90f05147f4219b0e64be11f43d3
https://doi.org/10.1002/prot.24552

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