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Journal Articles
- 2021
[j9]Pedro Matos-Filipe
, António J. Preto, Panagiotis I. Koukos, Joana Mourão, Alexandre M. J. J. Bonvin, Irina S. Moreira:
MENSAdb: a thorough structural analysis of membrane protein dimers. Database J. Biol. Databases Curation 2021 (2021)- [j8]Panagiotis I. Koukos, Manon Réau, Alexandre M. J. J. Bonvin:
Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. J. Chem. Inf. Model. 61(9): 4807-4818 (2021) - 2020
- [j7]Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci, Alexandre M. J. J. Bonvin, Attilio Vittorio Vargiu:
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. J. Comput. Aided Mol. Des. 34(2): 149-162 (2020) - 2019
- [j6]Anna Vangone, Jörg Schaarschmidt, Panagiotis I. Koukos, Cunliang Geng, Nevia Citro, Mikael E. Trellet, Li C. Xue, Alexandre M. J. J. Bonvin:
Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. Bioinform. 35(9): 1585-1587 (2019) - [j5]Brian Jiménez-García, Katarina Elez, Panagiotis I. Koukos, Alexandre M. J. J. Bonvin, Anna Vangone:
PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes. Bioinform. 35(22): 4821-4823 (2019) - [j4]Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin:
Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. J. Comput. Aided Mol. Des. 33(1): 83-91 (2019) - 2018
- [j3]Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, João P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone, Alexandre M. J. J. Bonvin:
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. J. Comput. Aided Mol. Des. 32(1): 175-185 (2018) - 2014
- [j2]Panagiotis I. Koukos, Nicholas M. Glykos:
On the Application of Good-Turing Statistics to Quantify Convergence of Biomolecular Simulations. J. Chem. Inf. Model. 54(1): 209-217 (2014) - 2013
- [j1]Panagiotis I. Koukos, Nicholas M. Glykos:
Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories. J. Comput. Chem. 34(26): 2310-2312 (2013)
Informal and Other Publications
- 2021
- [i1]Rodrigo Vargas Honorato, Panagiotis I. Koukos, Brian Jiménez-García, Andrei Tsaregorodtsev, Marco Verlato, Andrea Giachetti, Antonio Rosato, Alexandre M. J. J. Bonvin:
Structural biology in the clouds: The WeNMR-EOSC Ecosystem. CoRR abs/2107.01056 (2021)
Coauthor Index
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