TransAtlas:

Citing TransAtlas:

Pedro Sfriso, Adam Hospital, Diana Buitrago, Roberto Mosca, Agustí Emperador, Josep Lluís Gelpí, Patrick Aloy and Modesto Orozco;
TransAtlas: an integrative database of protein conformational transitions.
Submitted.

Coarse-Grained Discrete Molecular Dynamics:

Pedro Sfriso, Adam Hospital, Agustí Emperador, Modesto Orozco.
Exploration of Conformational Transition Pathways from Coarse-Grained Simulations.
Bioinformatics. (2013) 29(16):1980-6.

Pedro Sfriso, Agusti Emperador, Laura Orellana, Adam Hospital, Josep Lluis Gelpi and Modesto Orozco.
Finding conformational pathways from discrete molecular dynamics simulations.
J. Chem. Theory Comput., 2012, 8(11): 4707-4718.

Agusti Emperador, Oliver Carrillo, Manuel Rueda, Modesto Orozco.
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.
Biophysical Journal. (2008) 95, 2127-2138.

Molecular Visualizers:

Humphrey, W., Dalke, A. and Schulten, K.
VMD - Visual Molecular Dynamics.
J. of Molec. Graphics. (1996) 14, 33-38.

Jmol: an open-source Java viewer for chemical structures in 3D.
https://www.jmol.org/

Molecular Dynamics:

Adam Hospital, Pau Andrio, Carles Fenollosa, Damjan Cicin-Sain, Modesto Orozco, Josep Lluís Gelpí
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.
Bioinformatics, 2012, 28(9):1278-1279.

Tim Meyer, Marco D'Abramo, Adam Hospital, Manuel Rueda, Carles Ferrer-Costa, Alberto Pérez, Oliver Carrillo, Jordi Camps, Carles Fenollosa, Dmitry Repchevsky, Josep Lluís Gelpí, Modesto Orozco.
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.
Structure. (2010) 18(11), 1399-1409.

Mark James Abraham, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C. Smith, Berk Hess and Erik Lindahl.
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers.
SoftwareX. (2015) 1, 19-25.

Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi, Carlo Camilloni, Giovanni Bussi.
PLUMED 2: New feathers for an old bird.
Computer Physics Communications. (2014) 185(2), 604-613.