Abstract
BackgroundA 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.ResultsMORT 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.ConclusionsWe 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 http://cadd.suda.edu.cn/MORT/index.htm.
Highlights
Introduction to methodology and encoding rulesJ Chem Inf Comput Sci 1988, 28(1):31–36. 15
A lot of functionalities that should have been incorporated into XLEAP were either implemented as separate programs, such as ADDLES2 for Locally Enhanced Sampling, and antechamber for the calculations of partial charges and the assignment of atom types, or merged into molecular dynamics (MD) calculation stage as extra points
Molecular Objects and Relevant Templates (MORT) can be used as a foundational library to develop new programs or software packages for computational biology and computer-aided drug design (CADD)
Summary
MORT contains several advantages compared with the other libraries. MORT written in C++ natively supports the paradigm of object-oriented design, and it can be understood and extended . 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. A lot of functions have been included in this library, and a molecule can be manipulated at different levels. 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
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