Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories. - Panagiotis I. Koukos; Nicholas M. Glykos (J. Comput. Chem., 2013)

On the Application of Good-Turing Statistics to Quantify Convergence of Biomolecular Simulations. - Panagiotis I. Koukos; Nicholas M. Glykos (J. Chem. Inf. Model., 2014)

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. - 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; et al. (J. Comput. Aided Mol. Des., 2018)

PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes. - Brian Jiménez-García; Katarina Elez; Panagiotis I. Koukos; Alexandre M. J. J. Bonvin; Anna Vangone (Bioinform., 2019)

Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. - Anna Vangone; Jörg Schaarschmidt; Panagiotis I. Koukos; Cunliang Geng; Nevia Citro; Mikael E. Trellet; Li C. Xue; Alexandre M. J. J. Bonvin (Bioinform., 2019)

Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. - Panagiotis I. Koukos; Li C. Xue; Alexandre M. J. J. Bonvin (J. Comput. Aided Mol. Des., 2019)

Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. - Andrea Basciu; Panagiotis I. Koukos; Giuliano Malloci; Alexandre M. J. J. Bonvin; Attilio Vittorio Vargiu (J. Comput. Aided Mol. Des., 2020)

MENSAdb: a thorough structural analysis of membrane protein dimers. - Pedro Matos-Filipe; António J. Preto; Panagiotis I. Koukos; Joana Mourão; Alexandre M. J. J. Bonvin; Irina S. Moreira (Database J. Biol. Databases Curation, 2021)

Structural biology in the clouds: The WeNMR-EOSC Ecosystem. - Rodrigo Vargas Honorato; Panagiotis I. Koukos; Brian Jiménez-García; Andrei Tsaregorodtsev; Marco Verlato; Andrea Giachetti 002; Antonio Rosato; Alexandre M. J. J. Bonvin (CoRR, 2021)

Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. - Panagiotis I. Koukos; Manon Réau; Alexandre M. J. J. Bonvin (J. Chem. Inf. Model., 2021)