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5 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…
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…