Encyclopedia of Biophysics

Living Edition
| Editors: Gordon Roberts, Anthony Watts, European Biophysical Societies

HYDRO Suite of Computer Programs for Solution Properties of Rigid Macromolecules

  • José García de la TorreEmail author
  • José G. Hernández Cifre
  • Álvaro Ortega
Living reference work entry
DOI: https://doi.org/10.1007/978-3-642-35943-9_291-1



The HYDRO suite is a collection of computer tools for predicting hydrodynamic and other solution properties from macromolecular structures and to gather structural information from such properties.

A collection of free-domain, user-friendly, and well-documented computer programs to predict properties from the three-dimensional shape of rigid particles, with various level of resolution, from very coarse-grained models to atomic level.


Hydrodynamic properties, like translational and rotational diffusion, intrinsic viscosities, relaxation times, and other properties like those related to scattering of radiation, e.g., the radius of gyration or the distribution of distances, are, in the case of rigid particles, directly determined from their size and shape and are therefore potential sources of information about their overall structures. Thus,...

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  1. Ackerman CJ, Harnett MM, Harnett W, Kelly SM, Svergun DI, Byron O (2003) 19 Å solution structure of the filarial nematode immunomodulatory protein, ES-62. Biophys J 84:489–500CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bloomfield VA, Dalton WO, van Holde KE (1967) Frictional coefficients of multisubunit structures. Biopolymers 5:135–148CrossRefPubMedGoogle Scholar
  3. Frembgen-Kesner T, Elcock A (2009) Striking effects of hydrodynamic interaction on the simulated diffusion and folding of proteins. J Chem Theor Comput 5:242–256CrossRefGoogle Scholar
  4. García de la Torre J, Bloomfield VA (1981) Hydrodynamic properties of complex, rigid, biological macromolecules. Theory and applications. Q Rev Biophys 14:81–139CrossRefPubMedGoogle Scholar
  5. Garcia de la Torre J, del Rio Echenique G, Ortega A (2007) Calculation of rotational diffusion and intrinsic viscosity of bead models for macromolecules and nanoparticles. J Phys Chem B 111:955–961CrossRefPubMedGoogle Scholar
  6. García de la Torre J, Huertas ML, Carrasco B (2000a) Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys J 78:719–730CrossRefPubMedPubMedCentralGoogle Scholar
  7. García de la Torre J, Huertas ML, Carrasco B (2000b) HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations. J Magn Reson 147:138–146CrossRefPubMedGoogle Scholar
  8. García de la Torre J, Llorca O, Carrascosa JL, Valpuesta JM (2001) HYDROMIC: prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy. Eur Biophys J 30:457–462CrossRefPubMedGoogle Scholar
  9. Garcia de la Torre J, Carrasco B (2002) Hydrodynamic properties of rigid macromolecules composed of ellipsoidal and cylindrical subunits. Biopolymers 63:163–167CrossRefPubMedGoogle Scholar
  10. García de la Torre J, Ortega A, Amorós D, Rodríguez Schmidt R, Hernández Cifre JG (2010) Methods and tools for the prediction of hydrodynamic coefficients and other solution properties of flexible macromolecules in solution. A tutorial minireview. Macromol Biosci 10:721–730CrossRefPubMedGoogle Scholar

Copyright information

© European Biophysical Societies' Association (EBSA) 2018

Authors and Affiliations

  • José García de la Torre
    • 1
    Email author
  • José G. Hernández Cifre
    • 1
  • Álvaro Ortega
    • 1
  1. 1.Department of Physical ChemistryUniversity of MurciaMurciaSpain

Section editors and affiliations

  • Stephen E. Harding
    • 1
  • Mary Philips-Jones
  1. 1.School of Biosciences, NCMH LaboratoryUniversity of NottinghamSutton BoningtonUK