25 citations · 45 across the 3 of their papers we have counts for
5 papers
Structural biology in the clouds: The WeNMR-EOSC Ecosystem
Rodrigo Vargas Honorato, Panagiotis I. Koukos, Brian Jiménez-García +5
Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of…
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: Performance in pose prediction in the D3R-GC4
Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci +2
We report the performance of our newly introduced Ensemble Docking with Enhanced sampling of pocket Shape (EDES) protocol coupled to a template-based algorithm to generate near-nat…
MENSADB: A Thorough Structural Analysis of Membrane Protein Dimers
Pedro Matos-Filipe, António J. Preto, Panagiotis I. Koukos +3
Membrane Proteins (MPs) account for around 15-39% of the human proteome and assume a critical role in a vast set of cellular and physiological mechanisms, including molecular trans…
Clustering of molecular dynamics trajectories via peak-picking in multidimensional PCA-derived distributions
Athanasios S. Baltzis, Panagiotis I. Koukos, Nicholas M. Glykos
We describe a robust, fast, and memory-efficient procedure that can cluster millions of structures derived from molecular dynamics simulations. The essence of the method is based o…
On the application of Good-Turing statistics to quantify convergence of biomolecular simulations
Panagiotis I. Koukos, Nicholas M. Glykos
Quantifying convergence and sufficient sampling of macromolecular molecular dynamics simulations is more often than not a source of controversy (and of various ad hoc solutions) in…