These are softwares and web servers we contributed to develop:

PLUMED: an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics and quantum chemistry engines (GitHub).

PLUMED-NEST: is the public repository of the PLUMED consortium. It provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation (or analysis) contained in a published paper.

δ2D: A method of calculating secondary structures populations of proteins from their chemical shifts (GitHub).

s2D: A method of predicting protein secondary structure populations from the amino acid sequence.  This predicts simultaneously structure and intrinsic disorder. It includes polyproline-II prediction.

MobiDB: a database of protein disorder and mobility annotations. It also includes protein-protein interactions predictions.

FleXgeo: A package for protein conformational ensemble analyses based on a differential geometry representation of protein backbones.

In these repositories you can find the most common tools we use of our daily work, scripts, force fields, modified tools, as well as input files needed to reproduce some of our simulations