TY - JOUR
T1 - MORT
T2 - A powerful foundational library for computational biology and CADD
AU - Zhang, Qian
AU - Zhang, Wei
AU - Li, Youyong
AU - Wang, Junmei
AU - Zhang, Jian
AU - Hou, Tingjun
N1 - Funding Information:
This study was supported by the National Science Foundation of China (21173156), the National Basic Research Program of China (973 program, 2012CB932600), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).
PY - 2014/6/27
Y1 - 2014/6/27
N2 - 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.
AB - 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.
KW - AMBER
KW - Antechamber
KW - CADD
KW - Foundational library
KW - MORT
KW - Relational model
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U2 - 10.1186/1758-2946-6-36
DO - 10.1186/1758-2946-6-36
M3 - Article
AN - SCOPUS:84902907909
SN - 1758-2946
VL - 6
JO - Journal of Cheminformatics
JF - Journal of Cheminformatics
IS - 1
M1 - 36
ER -