1996-2009 All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the  before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or  re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.


 Online Journal of Bioinformatics



Volume 8 (1):45-55, 2007.

 Analysis of MMFF94x and AMBER99 force fields using aspartic, serine metallo-proteases

and sugar-binding protein data sets.


Singh H, Marla SS, Verma D


Biotechnology and Bioinformatics Department, Jaypee University of Information Technology, Waknaghat, Solan (H.P.) India 173215




Singh H, Marla SS, Verma D, Analysis of MMFF94x and AMBER99 force fields using aspartic, serine, metallo-proteases and sugar-binding protein data sets, Onl J Bioinform., 8 (1) 45-55, 2007. Force fields vary in that they are developed to be applied to different aspects of bio-organic chemistry. They are all developed differently and with specific sets of data. It has been found that although there are significant differences in modern day force fields, they all perform at the same magnitude of precision. Although there are differences but each one has its own strength due to the intended application during development and the data sets used to derive and parameterize them. In this work MMFF94x & AMBER99 force fields were applied for energy minimization on proteins belonging to different classes e.g. Aspartic Proteases, Serine Proteases, Metallo-proteases, Sugar-binding proteins. Since both the force fields are successful in their respective terms, a question remains unanswered; Out of the two, MMFF94 & AMBER, which force field should we use for energy minimization of proteins? In this study we have tried to evaluate this question by dividing the proteins in their respective classes, finding their initial and final energies and finally applying statistical techniques (paired test). This was done by using MOE (Molecular Operating Environment) software Package from Chemical Computing Group. It was observed that the selection of force field should be on the basis of class of protein to which that protein belongs.


Keywords- Forcefields, AMBER99, MMF94X.