25 citations · 38 across the 8 of their papers we have counts for
8 papers
Quantifying the uncertainty of molecular dynamics simulations : Good-Turing statistics revisited
Vasiliki Tsampazi, Nicholas M. Glykos
We have previously shown that Good-Turing statistics can be applied to molecular dynamics trajectories to estimate the probability of observing completely new (thus far unobserved)…
Atomic Density Distributions in Proteins: Structural and Functional Implications
Sotirios Touliopoulos, Nicholas M. Glykos
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the…
The curious case of A31P, a topology-switching mutant of the Repressor of Primer protein : A molecular dynamics study of its folding and misfolding
Olympia-Dialekti Vouzina, Alexandros Tafanidis, Nicholas M. Glykos
The effect of mutations on protein structures is usually rather localized and minor. Finding a mutation that can single-handedly change the fold and/or topology of a protein struct…
Folding Molecular Dynamics Simulations of the Transmembrane Peptides of Influenza A, B M2, and MERS-, SARS-CoV E Viral Proteins
Antonios Kolocouris, Isaiah Arkin, Nicholas M. Glykos
Viroporins are small viral proteins that oligomerize in the membrane of host cells and induce the formation of hydrophilic pores in these membranes, thus altering the physiological…
Folding molecular dynamics simulation of T-peptide, a HIV viral entry inhibitor : Structure, dynamics, and comparison with the experimental data
Ioanna Gkogka, Nicholas M. Glykos
Peptide T is a synthetic octapeptide fragment, which corresponds to the region 185-192 of the gp120 HIV coat protein and functions as a viral entry inhibitor. In this work, a foldi…
On the propensity of Asn-Gly-containing heptapeptides to form -turn structures : comparison between ab initio quantum mechanical calculations and Molecular Dynamics simulations
Dimitrios A. Mitsikas, Nicholas M. Glykos
Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same pe…
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…