The lab’s research is helped by the strong commitment in developing new tools.
Adun
Adun is a new extendible molecular simulation program that also includes data management and analysis capabilities. The Adun molecular simulation application has been designed from the ground up to cater for a broad range of users and needs, from computational chemists to experimental biologists. Adun provides advanced algorithms and protocols for molecular simulation which can be accessed from an intuitive user interface but also from a more flexible programmatic level. It is built on the Adun framework which is a powerful library for creating and manipulating simulations. However it goes beyond just performing simulations by incorporating tools for analysis and management of simulation data aswell as providing mechanisms that allow the easy extension of its abilities. In many senses Adun is simply a structure that can incorporate any molecular simulation tools allowing it almost unlimited potential for growth.
[bibtex file=jordi.bib key=Avila2011] [bibtex file=jordi.bib key=Johnston2009] [bibtex file=jordi.bib key=Johnston2007] [bibtex file=jordi.bib key=Johnston2005b]ByoDyn
In systems biology it is becoming a routine task to build models of increasing complexity on a given biochemical network or pathway of interest. One of the main problems in building such models is the determination of the parameters underlying each modelled process. ByoDyn has been designed to provide an easily extendable computational framework to estimate and analyze parameters in highly uncharacterized models.
[bibtex file=jordi.bib key=Lomana2008]MIPSim
MIPSim (Molecular Interaction Potential Similarity) is a computer package that calculates both quantum and classical MIPs of biomolecules and makes comparisons and superpositions based on them. The program is opensource although its development is currently discontinued in the lab. More efforts will be done in the (near?) future
[bibtex file=jordi.bib key=Barbany2005] [bibtex file=jordi.bib key=Sanz2002] [bibtex file=jordi.bib key=Caceres2000]Other software
Extensive work has been also carried out in a number of software tools for computational chemistry.
- MC-TINKERRATE: a program for multiconfigurational molecular mechanics.
[bibtex file=jordi.bib key=Albu2009] - POLYRATE: a program for variational transition state theory (VTSTS) calculations.
[bibtex file=jordi.bib key=Zheng2008] - MOLARIS: a computational biochemistry tool for the study of energetics and dynamics of proteins. Check the theory and reference manuals of the program by accessing the following links: