Martini & Gromacs & VMD & Bendix (and ROP)

 Have been playing with the Martini force field for some time now. Still digging. Here is a short movie of a ROP mutant using Martini & Gromacs, and visualized with VMD & Bendix.

Just came out ...

«A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations.»

https://doi.org/10.1371/journal.pone.0243429

Illustrating transitions between conformers using circos plots

A new tutorial  is available for preparing a circos plot illustrating the transitions between stable conformers identified from e.g. a folding molecular dynamics simulation.

Short‐range periodicities paper.

Just came out : "On the presence of short‐range periodicities in protein structures that are not related to established secondary structure elements", https://doi.org/10.1002/prot.25758

Molecular simulation of peptides review

Just came out : "Molecular simulation of peptides coming of age: Accurate prediction of folding, dynamics and structures"

http://doi.org/10.1016/j.abb.2019.01.033

Just came out : «An unusual α-carbon hydroxylation of proline promotes active-site maturation», JACS, http://pubs.acs.org/doi/abs/10.1021/jacs.6b12209

Force-field dependent secondary structure preferences

Weblogo representations of the per-residue secondary structure preferences (as produced by STRIDE) for folding simulations of the α-Lactalbumin-derived peptide studied in this paper. Results from seven force fields are shown. The experimental NMR results indicate a mostly 310-helical N-terminal part (residues 3-6) with an occupancy of ~50%, and a completely disordered C-terminus. The symbols in the weblogo diagrams are G => 310 helix, H => α helix, T => turn, C => random coil, E => extended. The force fields are CHARMM22, OPLSaa, AMBER ff12SB, AMBER ff99SB, and three variants of AMBER ff99SB (99SB-ILDN-NMR, 99SB-ILDN, 99SB-STAR-ILDN). It does look like a clear take-home message is present in these diagrams...

grcarma on the cover of JCC

The program grcarma written by Panagiotis Koukos made the cover story of the latest issue of the Journal of Computational Chemistry. Well done Panagiotis !

Homepage update

Added Kontopoulos' and Koukos' papers. Screenshots and artistic renderings follow ... :-)

Adaptive tempering & folding simulations

Playing with adaptive tempering using a very short (200 ns) folding simulation of the CLN025 decapeptide. Interesting diagrams, see this Norma page ...

Web-based service for GraphEnt

This is a fully automated web-based interface to the program GraphEnt which aims to simplify the calculation of maximum entropy protein electron density maps. The service is located at http://orion.mbg.duth.gr/graphent

BC0361 solved (!)

M.BseCI solved ...

Maximum entropy estimate of the current 2mFo-DFc electron density map
at a region encompassing portion of the DNA oligonucleotide.

Maximum entropy : seeing is believing ?

Harker sections from an anomalous Patterson function using 10-3.25 Angstrom data for a putative BseCI derivative. Conventional FFT to the right, maximum entropy reconstruction to the left. Seeing is believing even for M.BseCI ??? :-)

If you make it a little bit more difficult by using 6-3.25 Angstrom data, the signal completely disappears from the conventional :

Thankfully, when using all data between 15 and 3.5 Angstrom, the signal is obvious even in the conventional map: