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Trends in pharmacological sciences (Regular ed.), ISSN 0165-6147, 2015, Volume 36, Issue 2, pp. 78 - 95
Journal Article
Biophysical journal, ISSN 0006-3495, 2018, Volume 114, Issue 10, pp. 2271 - 2278
Ensemble docking corresponds to the generation of an “ensemble” of drug target conformations in computational structure-based drug discovery, often obtained by using molecular dynamics simulation, that is used in docking candidate ligands... 
ACCELERATED MOLECULAR-DYNAMICS | DESIGN | POTENT | PROTEIN | BIOPHYSICS | INDUCED FIT | INHIBITORS | SIMULATION | MARKOV STATE MODELS | RECEPTOR FLEXIBILITY | SOFTWARE | Drug Discovery - methods | Protein Conformation | Molecular Docking Simulation | Software | Kinetics | Molecular dynamics | Molecular biology | Drug discovery | BASIC BIOLOGICAL SCIENCES | Biophysical s
Journal Article
by Lensink, Marc F and Velankar, Sameer and Kryshtafovych, Andriy and Huang, Shen-You and Schneidman-Duhovny, Dina and Sali, Andrej and Segura, Joan and Fernandez-Fuentes, Narcis and Viswanath, Shruthi and Elber, Ron and Grudinin, Sergei and Popov, Petr and Neveu, Emilie and Lee, Hasup and Baek, Minkyung and Park, Sangwoo and Heo, Lim and Rie Lee, Gyu and Seok, Chaok and Qin, Sanbo and Zhou, Huan-Xiang and Ritchie, David W and Maigret, Bernard and Devignes, Marie-Dominique and Ghoorah, Anisah and Torchala, Mieczyslaw and Chaleil, Raphaël A.G and Bates, Paul A and Ben-Zeev, Efrat and Eisenstein, Miriam and Negi, Surendra S and Weng, Zhiping and Vreven, Thom and Pierce, Brian G and Borrman, Tyler M and Yu, Jinchao and Ochsenbein, Françoise and Guerois, Raphaël and Vangone, Anna and Rodrigues, João P.G.L.M and van Zundert, Gydo and Nellen, Mehdi and Xue, Li and Karaca, Ezgi and Melquiond, Adrien S.J and Visscher, Koen and Kastritis, Panagiotis L and Bonvin, Alexandre M.J.J and Xu, Xianjin and Qiu, Liming and Yan, Chengfei and Li, Jilong and Ma, Zhiwei and Cheng, Jianlin and Zou, Xiaoqin and Shen, Yang and Peterson, Lenna X and Kim, Hyung-Rae and Roy, Amit and Han, Xusi and Esquivel-Rodriguez, Juan and Kihara, Daisuke and Yu, Xiaofeng and Bruce, Neil J and Fuller, Jonathan C and Wade, Rebecca C and Anishchenko, Ivan and Kundrotas, Petras J and Vakser, Ilya A and Imai, Kenichiro and Yamada, Kazunori and Oda, Toshiyuki and Nakamura, Tsukasa and Tomii, Kentaro and Pallara, Chiara and Romero-Durana, Miguel and Jiménez-García, Brian and Moal, Iain H and Férnandez-Recio, Juan and Joung, Jong Young and Kim, Jong Yun and Joo, Keehyoung and Lee, Jooyoung and Kozakov, Dima and Vajda, Sandor and Mottarella, Scott and Hall, David R and Beglov, Dmitri and Mamonov, Artem and Xia, Bing and Bohnuud, Tanggis and Del Carpio, Carlos A and Ichiishi, Eichiro and Marze, Nicholas and Kuroda, Daisuke and Roy Burman, Shourya S and Gray, Jeffrey J and Chermak, Edrisse and Cavallo, Luigi and Oliva, Romina and ...
Proteins, structure, function, and bioinformatics, ISSN 0887-3585, 2016, Volume 84, Issue S1, pp. 323 - 348
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... 
Oligomer state | CASP | Molecular Biology | Structural Biology | CAPRI | Blind prediction | Biochemistry | Protein docking | Protein interaction | protein interaction | blind prediction | protein docking | oligomer state | DESIGN | BIOCHEMISTRY & MOLECULAR BIOLOGY | ALGORITHM | ALIGN | BIOPHYSICS | AFFINITY | SERVER | ZDOCK | Proteins | Protein-protein docking | Heteroprotein | Enginyeria biomèdica | Proteïnes | Investigació | CAPRI Round 30 | Homoprotein | Àrees temàtiques de la UPC | Protein binding
Journal Article
Journal of molecular biology, ISSN 0022-2836, 2015, Volume 427, Issue 19, pp. 3031 - 3041
Journal Article
Bioinformatics, ISSN 1367-4803, 06/2014, Volume 30, Issue 12, pp. 1771 - 1773
... be modeled to obtain an understanding of their molecular basis. We present a user-friendly protein docking server, based on the rigidbody docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | PERFORMANCE | CAPRI | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | ZRANK | WEB SERVER | Molecular Docking Simulation - methods | Multiprotein Complexes - chemistry | Software | Algorithms | Protein Multimerization | Applications Notes
Journal Article
Molecules (Basel, Switzerland), ISSN 1420-3049, 2018, Volume 23, Issue 11, p. 3018
...–peptide docking and molecular dynamics (MD) simulation. Based on the equilibrated MD trajectory, the total binding free energy between GluN2B-CT1290-1310 and DAPK1 was computed... 
MD simulation | TARGET | BINDING MECHANISM | DAPK1-GluN2B peptide | hotspot | binding free energy | BIOCHEMISTRY & MOLECULAR BIOLOGY | KINASE | RECEPTOR | FORCE-FIELDS | IDENTIFICATION | ENRICHED RESOURCE | CHEMISTRY, MULTIDISCIPLINARY | SUBUNIT ARRANGEMENT | ENERGETIC BASIS | UPDATE | protein-peptide docking | protein–peptide docking
Journal Article