Computing is any goal-oriented activity requiring, benefiting from, or creating computing machinery. It includes the study and experimentation of algorithmic processes, and the development of both hardware and software. Computing has scientific, engineering, mathematical, technological, and social aspects. Major computing disciplines include computer engineering, computer science, cybersecurity, data science, information systems, information technology, and software engineering.
Software consists of computer programs that instruct the execution of a computer.
Software design is the process of conceptualizing how a software system will work before it is implemented or modified. Software design also refers to the direct result of the design process – the concepts of how the software will work which consists of both design documentation and undocumented concepts.
Software development is the process used to create software. Programming and maintaining the source code is the central step of this process, but it also includes conceiving the project, evaluating its feasibility, analyzing the business requirements, software design, testing, to release. Software engineering, in addition to development, also includes project management, employee management, and other overhead functions. Software development may be sequential, in which each step is complete before the next begins, but iterative development methods where multiple steps can be executed at once and earlier steps can be revisited have also been devised to improve flexibility, efficiency, and scheduling.
GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software released under the GNU Lesser General Public License (LGPL).
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.
MOPAC is a computational chemistry software package that implements a variety of semi-empirical quantum chemistry methods based on the neglect of diatomic differential overlap (NDDO) approximation and fit primarily for gas-phase thermochemistry. Modern versions of MOPAC support 83 elements of the periodic table and have expanded functionality for solvated molecules, crystalline solids, and proteins.
PyMOL is a source-available molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license, and some of the source code is no longer released. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.
Amsterdam Density Functional (ADF) is a program for first-principles electronic structure calculations that makes use of density functional theory (DFT). ADF was first developed in the early seventies by the group of E. J. Baerends from the Vrije Universiteit in Amsterdam, and by the group of T. Ziegler from the University of Calgary. Nowadays many other academic groups are contributing to the software. Software for Chemistry & Materials (SCM), formerly known as Scientific Computing & Modelling is a spin-off company from the Baerends group. SCM has been coordinating the development and distribution of ADF since 1995. Together with the rise in popularity of DFT in the nineties, ADF has become a popular computational chemistry software package used in the industrial and academic research. ADF excels in spectroscopy, transition metals, and heavy elements problems. A periodic structure counterpart of ADF named BAND is available to study bulk crystals, polymers, and surfaces. The Amsterdam Modeling Suite has expanded beyond DFT since 2010, with the semi-empirical MOPAC code, the Quantum ESPRESSO plane wave code, a density-functional based tight binding (DFTB) module, a reactive force field module ReaxFF, and an implementation of Klamt's COSMO-RS method, which also includes COSMO-SAC, UNIFAC, and QSPR.
The Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, which performs common tasks in molecular modelling.
The Molecular Modeling Toolkit is a library that implements common molecular simulation techniques, with an emphasis on biomolecular simulations. It uses modern software engineering techniques in order to overcome limitations associated with the large monolithic simulation programs that are commonly used for biomolecules. Its principal advantages are (1) easy extension and combination with other libraries due to modular library design, (2) a single high-level general-purpose programming language (Python) is used for library implementation as well as for application scripts, (3) use of documented and machine-independent formats for all data files, and (4) interfaces to other simulation and visualization programs.
BALL is a C++ class framework and set of algorithms and data structures for molecular modelling and computational structural bioinformatics, a Python interface to this library, and a graphical user interface to BALL, the molecule viewer BALLView.
Tinker, previously stylized as TINKER, is a suite of computer software applications for molecular dynamics simulation. The codes provide a complete and general set of tools for molecular mechanics and molecular dynamics, with some special features for biomolecules. The core of the software is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives via straightforward means.
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo.
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture.
KeyCreator is a commercial software application for 2D and 3D computer-aided design (CAD) and drafting available since 2004.
FlexAID is a molecular docking software that can use small molecules and peptides as ligands and proteins and nucleic acids as docking targets. As the name suggests, FlexAID supports full ligand flexibility as well side-chain flexibility of the target. It does using a soft scoring function based on the complementarity of the two surfaces.
