Version 10, September 2011

A. Ortega, D. Amorós, J. Garc1a de la Torre, "Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models" Biophys. J. 101, 892-898 (2011) [see also Supporting Information available in the journal's web site]

HYDROPRO computes the hydrodynamic properties of rigid macromolecules (proteins, small nucleic acids, macromolecular complexes, etc.) from their structure, as specified by the coordinates taken from a PDB file supplied by the user, from which the proper hydrodynamic model is built by the program itself. The HYDROPRO calculation comprises the basic hydrodynamic properties: translational diffusion coefficient, sedimentation coefficient, intrinsic viscosity, and relaxation times, along with the radius of gyration. Optionally, HYDROPRO computes also other solution properties such as the covolume (related to the second virial coefficient) and scattering related properties such as the angular dependence of scattering intensities and the distribution of intramolecular distances. Beware that we have another similar program – HYDRONMR – for the more specific purpose of calculating quantities relevant in NMR relaxation.

HYDROPRO now accepts, in addition to atomic-level structures, also more coarse-grained residue-level structures that are specified by the position of residues, given by C-alpha coordinates

Also, in addition to the shell-model methodology, HYDROPRO may also work with a bead-model calculation, with one bead per structural element (atom or residue), which is a bit less accurate but more computationally efficient for structures with a few hundred of such structural elements.

HYDROPRO has been entirely rewritten in Fortran 90, in order to take advantage of dynamic memory allocation, which greatly increases the reach of the program, and optimizes the computational efficiency in modern multi-core architectures nowadys available even in simple PCs.

Typical computing times, of about 3 minutes in the previous version are now of about 10 seconds. And the program can treat extremely large macromolecular structures (up to the 70S ribosome!)

And, last, but not least, HYDROPRO now comes with a Graphical User interface (GUI) for Windows, which makes the use of the program - which was already quite simple ! -even more user-frindly, ideal for occasional users, teaching, etc. Of course, the file-driven version will be most appropriate for serial, high-throughput applications.

For more details, see the HYDROPRO User Guide

Files for download:

hydropro10.pdf PDF User Guide
hydropro10.zip WinZip All files in compressed folder
hydropro10contents.txt ASCII Contents of the zip file
WinHydropro10.pdf PDF User Guide
WinHydropro10.zip WinZip All files in compressed folder
WinHydropro10contents.txt ASCII Contents of the zip file

Return to Computer programs