Instant Access to the Journals you Need

Read Online + Print Articles, for just $40 a month.

Get 2 Weeks Free

ProMode: a database of normal mode analyses on protein molecules with a full-atom model

ProMode: a database of normal mode analyses on protein molecules with a full-atom model

Abstract

Abstract Motivation: Although information from protein dynamics simulation is important to understand principles of architecture of a protein structure and its function, simulations such as molecular dynamics and Monte Carlo are very CPU-intensive. Although the ability of normal mode analysis (NMA) is limited because of the need for a harmonic approximation on which NMA is based, NMA is adequate to carry out routine analyses on many proteins to compute aspects of the collective motions essential to protein dynamics and function. Furthermore, it is hoped that realistic animations of the protein dynamics can be observed easily without expensive software and hardware, and that the dynamic properties for various proteins can be compared with each other. Results: Pro Mode, a database collecting NMA results on protein molecules, was constructed. The NMA calculations are performed with a full-atom model, by using dihedral angles as independent variables, faster and more efficiently than the calculations using Cartesian coordinates. In Pro Mode, an animation of the normal mode vibration is played with a free plug-in, Chime (MDL Information Systems, Inc.). With the full-atom model, the realistic three-dimensional motions at an atomic level are displayed with Chime. The dynamic domains and their mutual screw motions defined from the NMA results are also displayed. Properties for each normal mode vibration and their time averages, e.g. fluctuations of atom positions, fluctuations of dihedral angles and correlations between the atomic motions, are also presented graphically for characterizing the collective motions in more detail. Availability: http://promode.socs.waseda.ac.jp Bioinformatics 20(13) © Oxford University Press 2004; all rights reserved.
Loading next page...
 
/lp/oxford-university-press/promode-a-database-of-normal-mode-analyses-on-protein-molecules-with-a-h0evaABD7t

You're reading a free preview. Subscribe to read or print the entire article.

And millions more from thousands of peer-reviewed journals, for just $40/month.

Get 2 Weeks Free

To be the best researcher, you need access to the best research

  • With DeepDyve, you can stop worrying about how much articles cost, or if it's too much hassle to order — it's all at your fingertips. Your research is important and deserves the top content.
  • Read from thousands of the leading scholarly journals from Springer, Elsevier, Nature, IEEE, Wiley-Blackwell and more.
  • All the latest content is available, no embargo periods.

Stop missing out on the latest updates in your field

  • We’ll send you automatic email updates on the keywords and journals you tell us are most important to you.
  • There is a lot of content out there, so we help you sift through it and stay organized.