Bioinformatics software programs and tools (open-source)

Various kinds of bioinformatics software are available for free, for computational and molecular modeling which is applicable for Visualization, Docking, Chemical Drawing, Energy minimization, or understanding the molecular mechanism.

Free and open-source software are those that anyone can access freely for any purpose, study the software, and academic research or commercial purpose.

Bioinformatics open-source software programs and tools
Bioinformatics open-source software programs and tools

Some of the free open-source software for computational and Molecular modeling are given below:

Bioinformatics software/programs for visualization

Rasmol:

Rasmol is a computer visualization software program used for the study and display of biological macromolecules like Protein structure, nucleic acids, and small molecules. Rasmol visualization molecular tool was created by Roger Sayle in 1992 and used by many users for extraction of quality of images for their publications. Rasmol can be operated in different operating systems like Microsoft Windows, Apple Macintosh, UNIX, and VMS systems. The link for this software is here (http://www.openrasmol.org/).

Molvis: 

Molvis also called the molecular visualization tool is used for the discussion and study of molecular visualization software like FirstGlance in Jmol, Jmol, MDL Chime, Rasmol, protein explorer, and PyMol. It can be classified into two different types: stand-alone software and web-based tools (applets, plug-ins, or server-side programs).

PyMol:

PyMol is a user-sponsored molecular visualization system, used for the three-dimensional (3D) visualization of biomolecules like proteins, small molecules, nucleic acids, surfaces, electron densities, and trajectories. It is a molecular graphics system designed for real-time visualization and rapid generation of high-quality images and animations. Pymol is a highly powerful program and most of the molecular structures during research are developed by the use of this program. The link to this software is here (https://pymol.org/2/).

Jmol:

Jmol is a free, open-source molecule viewer in chemistry and biochemistry available for viewers and all researchers. It is a java based open source program for viewing chemical structures in 3D and also other crystals, materials, and biomolecules. It can be supported by Microsoft Windows, Mac OS X, and Linux systems. To cite Jmol ( http://www.jmol.org/).

DeepView:

DeepView, in the past also known as Swiss-PDBViewer, is a powerful molecular viewer that allows the analysis of several proteins at the same time. It can be used for structural alignments, homology modeling, energy minimization, mutating molecular models, and many other modeling tasks. It is a free program developed by Glaxo Smith Kline RD and the Swiss Institute of Bioinformatics. Amino acid mutation, H-Bonds, angles, and distance between the atoms are easy to obtain from the deep view program. To get access to DeepView (http://us.expasy.org/spdbv/).

gOpenMol:

gOpenMol is also a molecular visualization tool, for the visualization and analysis of molecular structures and their chemical properties. It was written by Leif Laaksonen and its version is available for Windows, Linux, and some Unix platforms. gOpenMol can be used with a quantum chemistry/molecular mechanics program. Site link to download gOpenMol (https://docs.csc.fi/apps/).

AstexViewer:

AstexViewer is used for the visualization of structure-based drug design and is a Java-based molecular graphics program. It is used for displaying molecular structure and electron density maps. It has been developed to study protein-ligand complex and does not produce high intended molecular graphics. It is very useful for the structural biology community. Get access to AstexViewer (https://bio.tools/openastexviewer). 

UCSF Chimera:

UCSF Chimera is one of the important visualization programs for the analysis of molecular structure and data related to it including sequence alignment, trajectories, density maps, docking results, supramolecular assemblies, and conformational ensembles. To get access to UCSF Chimera (https://www.cgl.ucsf.edu/chimera/).

Bioinformatics software/programs for DOCKING

DOCK:

DOCK is a docking software program generally used to address small molecules. Docking is the identification of low-energy binding modes of small molecules or ligand with the active site of a macromolecule or receptor with a known structured molecule. DOCK is applicable for predicting the binding mode of small molecule-protein complexes or searching for a database of ligands for compounds that inhibit enzyme activity, for a compound that binds to a particular protein, a compound that binds to nucleic acid targets, or to see the possibility of protein-protein interactions. It uses a geometric matching algorithm to superimpose the ligand onto a negative image of the binding pocket.

AutoDock:

AutoDock is the automated molecular modeling tool to model the ligand with full conformational flexibility. AutoDock is a useful simulation software that is designed to predict interactions of the small molecules such as substrate or drugs, binding to a receptor of known 3D structure. The modification to this software tool is done to add new functionalities. AutoDock 4 and AutoDock vina are the two-generation software of AutoDock.

FRED:

Fast Exhaustive Docking (FRED) is a software tool that performs a non-stochastic and systematic examination of all possible protein-ligand poses, filters for shape complementarity, and chemical feature alignment before selecting and optimizing poses. It uses Chemgauss 4 scoring function and Grapheme toolkit. It is also considered one of the fastest docking tools.

FTDock: 

FTDock is an algorithm for docking rigid molecules. It represents the two molecules onto orthogonal grids and performs a global scan of rotational and transitional space. The scoring method is primarily a surface complementary score between two grids. FTDock performs docking on two biomolecules in order to predict their correct binding geometry.

eHiTS:

eHiTS is an exhaustive and systematic docking tool that simplifies the drug design workflow with the help of its automated features. It produces highly accurate docking poses for virtual-throughput screening.

Bioinformatics software/programs for Energy Minimization

GAMESS:

GAMES (Generalized Atomic and Molecular Structure) is an energy minimization software program that displays the animations of Molecular structure, reaction paths, the normal mode of vibrations, total electron density, molecular electrostatic potentials, and density differences.

TINKER:

The tinker software is a modular molecular mechanics and dynamics package. A wide variety of force fields, including the modern polarizable atomic multipole-based AMOEBA model, is supported by it. This package is supported by Linux, Windows, and macOS. It also includes Force Field Explorer which is a tightly integrated Java-based graphical user interface that provides molecular visualization capabilities as well as the ability to launch and calculate Tinker calculations.

Bioinformatics software/programs for Software libraries

Molecular Modeling Toolkit:

The molecular modeling toolkit is an open-source program library for molecular simulation applications. It is developed using a high-level object-oriented general-purpose programing language called python for rapid code development and testing. It is based on an object-oriented model of a molecular system. Molecular Modeling Toolkit includes the construction of a molecular system for the support of proteins and nucleic acids, visualization, animations of dynamic trajectories and normal modes, molecular surface calculations, and energy minimization.

Chemistry Development Kit:

The Chemical Development Kit is an open-source java-based program for processing chemical information (cheminformatics). It provides the data structure to represent chemical concepts along with methods to manipulate such structures and perform computations on them. It is used for Drug Discovery, metabolism, and toxicology as this library implements a wide range of cheminformatics algorithms. Its areas in cheminformatics include molecule and reaction valence bond representation, coordinate generation and rendering, substructure SMARTS pattern searching, etc. 

Open Babel:

Open Babel is an open-source library designed to speak the many languages of chemical data. It allows anyone to search, convert, analyze, or store data from molecular modeling, solid-state materials, biochemistry, chemistry, or other related areas as it is an open and collaborative project. It can read, write and convert chemical file formats, filter and search molecular files using SMARTS and other methods, and supports molecular modeling cheminformatics, and bioinformatics.  Open Babel operates on Windows, Linux, and MacOSX.

Bioinformatics software/programs for chemical drawing

ACD/labs chem sketch:

ACD/lab chem sketch is an open-source program used for drawing chemical structures, including organics, organometallics, polymers, and Markush structures. It is also used to calculate molecular properties (molecular weight, density, molar refractivity, and more.

JSME Editor:

JSME is a free molecular editor written in JavaScript that supports the drawing and editing of molecules. It can be supported on desktops as well as on hand-held devices such as iPhones. JME applet is one of the most popular tools for molecular structure input on the web.

XDraw Chem:

XDraw Chem is a molecule drawing program in a two-dimensional structure for Unix Operating System. It is similar to other molecule drawing programs such as ChemDraw where it can read and write MDL Molfiles, binary files, and create images in popular formats like PNG and EPS. It is supported on Linux, Windows, and Mac OS X.

ISIS/Draw:

ISIS/Draw is somewhat similar to ChemDraw and is a chemical drawing program developed by the MDL information system. It is an intelligent drawing program that understands valance limits, bond angles, and aromatic ring system which makes users create chemical graphics in 2D or 3D form. It can be used to draw complicated structures like DNA, RNA, and amino acid sequences using this tool. It also helps to create many types of polymer structures, including homopolymers, source-based polymers, structure-based polymers, co-polymers, cross-linked polymers, branched polymers, random, and unspecified copolymers.

References

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  3. Yuan, S., Chan, H.S. and Hu, Z. (2017), Using PyMOL as a platform for computational drug design. WIREs Comput Mol Sci, 7: e1298.
  4. Hartshorn MJ. AstexViewer: a visualisation aid for structure-based drug design. J Comput Aided Mol Des. 2002 Dec;16(12):871-81.
  5. Zsoldos Z, Reid D, Simon A, Sadjad SB, Johnson AP. eHiTS: a new fast, exhaustive flexible ligand docking system. J Mol Graph Model. 2007 Jul;26(1):198-212. 
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  8. Willighagen, E.L., Mayfield, J.W., Alvarsson, J. et al. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J Cheminform 9, 33 (2017).
  9. Bienfait, B., Ertl, P. JSME: a free molecule editor in JavaScript. J Cheminform 5, 24 (2013).
  10. http://www.bioinformatics.org/mm/listinfo/molvis-list
  11. https://www.bioinformatics.org/wiki/Molecular_visualization
  12. http://www.geneinfinity.org/sp/sp_structmolvis.html
  13. http://jmol.sourceforge.net/
  14. http://www.virology.wisc.edu/acp/tutorials/DeepView.pdf
  15. https://deep-view.software.informer.com/
  16. https://sites.google.com/site/rangsiman1993/comp-chem/molecular-visualizations/gopenmol-elec-density-pes
  17. https://chem.utah.edu/directory/anderson/research-group/gopen/
  18. http://signe.teokem.lu.se/ulf/Methods/gopenmol.html
  19. http://www.sb.fsu.edu/~xray/Manuals/CCP4/AstexViewer_man/AstexViewer.html
  20. https://dock.compbio.ucsf.edu/Overview_of_DOCK/index.htm
  21. https://autodock.scripps.edu/
  22. https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/autodock
  23. http://www.sbg.bio.ic.ac.uk/docking/index.html
  24. https://www.sas.upenn.edu/~lineje/gamess.html
  25. https://hal.archives-ouvertes.fr/hal-01820747/document
  26. http://dirac.cnrs-orleans.fr/MMTK.html
  27. https://openbabel.org/docs/dev/Installation/install.html
  28. http://openbabel.org/wiki/Main_Page
  29. https://www.acdlabs.com/resources/free-chemistry-software-apps/chemsketch-freeware/
  30. https://jsme-editor.github.io/
  31. https://www.woodsidelabs.com/chemistry/xdrawchem.php
  32. https://www-jmg.ch.cam.ac.uk/cil/SGTL/MDL/ISISdraw.html

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