MORT: A powerful foundational library for computational biology and CADD

Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang, Jian Zhang, Tingjun Hou

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Background: A foundational library called MORT (Molecular Objects and Relevant Templates) for the development of new software packages and tools employed in computational biology and computer-aided drug design (CADD) is described here. Results: MORT contains several advantages compared with the other libraries. Firstly, MORT written in C++ natively supports the paradigm of object-oriented design, and thus it can be understood and extended easily. Secondly, MORT employs the relational model to represent a molecule, and it is more convenient and flexible than the traditional hierarchical model employed by many other libraries. Thirdly, a lot of functions have been included in this library, and a molecule can be manipulated easily at different levels. For example, it can parse a variety of popular molecular formats (MOL/SDF, MOL2, PDB/ENT, SMILES/SMARTS, etc.), create the topology and coordinate files for the simulations supported by AMBER, calculate the energy of a specific molecule based on the AMBER force fields, etc. Conclusions: We believe that MORT can be used as a foundational library for programmers to develop new programs and applications for computational biology and CADD. Source code of MORT is available at.

Original languageEnglish (US)
Article number36
JournalJournal of Cheminformatics
Volume6
Issue number1
DOIs
StatePublished - Jun 27 2014

Fingerprint

biology
drugs
templates
drug
Pharmaceutical Preparations
Molecules
manned orbital laboratories
programmers
molecules
Software packages
files
field theory (physics)
format
Topology
topology
paradigm
computer programs
energy
simulation

Keywords

  • AMBER
  • Antechamber
  • CADD
  • Foundational library
  • MORT
  • Relational model

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Computer Science Applications
  • Library and Information Sciences

Cite this

MORT : A powerful foundational library for computational biology and CADD. / Zhang, Qian; Zhang, Wei; Li, Youyong; Wang, Junmei; Zhang, Jian; Hou, Tingjun.

In: Journal of Cheminformatics, Vol. 6, No. 1, 36, 27.06.2014.

Research output: Contribution to journalArticle

Zhang, Qian ; Zhang, Wei ; Li, Youyong ; Wang, Junmei ; Zhang, Jian ; Hou, Tingjun. / MORT : A powerful foundational library for computational biology and CADD. In: Journal of Cheminformatics. 2014 ; Vol. 6, No. 1.
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