Gourt > Science > Biology > Biochemistry and Molecular Biology > Biomolecules > Software
Computer software (or simply software) is the programs and procedures that enable a computer to perform a specific task, as opposed to the physical components of the system (hardware). This includes application software such as a word processor, which enables a user to perform a task, and system software such as an operating system, which enables other software to run properly, by interfacing with hardware and with other software.
The term "software" was first used in this sense by John W. Tukey in 1957. In computer science and software engineering, computer software is all information processed by computer systems, programs and data. The concept of reading different sequences of instructions into the memory of a device to control computations was invented by Charles Babbage as part of his difference engine. The theory that is the basis for most modern software was first proposed by Alan Turing in his 1935 essay Computable numbers with an application to the Entscheidungsproblem. Hally, Mike (2005:79). Electronic brains/Stories from the dawn of the computer age. British Broadcasting Corporation and Granta Books, London. ISBN 1-86-207663-4.
Relationship to hardware
Computer software is so called in contrast to computer hardware, which encompasses the physical interconnections and devices required to store and execute (or run) the software. In computers, software is loaded into RAM and executed in the central processing unit. At the lowest level, software consists of a machine language specific to an individual processor. A machine language consists of groups of binary values signifying processor instructions (object code), which change the state of the computer from its preceding state. Software is an ordered sequence of instructions for changing the state of the computer hardware in a particular sequence. It is generally written in high-level programming languages that are easier and more efficient for humans to use (closer to natural language) than machine language. High-level languages are compiled or interpreted into machine language object code. Software may also be written in an assembly language, essentially, a mnemonic representation of a machine language using a natural language alphabet. Assembly language must be assembled into object code via an assembler. More on [ Computer software ]
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Amber - A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
Meta Description: [ Amber is a package of programs for
molecular dynamics simulations of proteins and nucleic acids ]
AMMP - A free program suite for molecular mechanics, dynamics and modeling with some special features like docking or ab initio DFT calculations. Runs under Linux/Unix and Win9x. The site provides access to the documentation and offers on-line tutorials.
AutoDock - A suite of automated docking tools. It is designed to predict how small flexible molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
Meta Description: [ AutoDock web site ]
B: On-line Molecular Modeling - B (formerly known as Biomer) is a Java-based molecular modeling program for small organic molecules and biopolymers. Supports nucleic acids (DNA/RNA), polypeptides, polysaccharides, the AMBER force field, geometry optimization, simulated annealing. Exports jpeg, gif, and ppm images.
Meta Description: [ B: A free web-based biomolecular modeling program. ]
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BioAdviser - Package for displaying, analyzing, and manipulating 3D structures of biological macromolecules, with special emphasis on the study of proteins and enzymes. Includes links to other products by FQS Poland, in Krakow.
Meta Description: [ BioAdviser 1.0 is novel super-fast software package for displaying, analyzing, and manipulating 3-D structures of biological macromolecules, with special emphasis on the study of proteins and enzymes. ]
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CHARMM - A program for macromolecular dynamics and mechanics. It performs standard molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation and periodic images.
ChemVis - Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany.
D - PSCAN, PMOL2Q, DBFILTER download page. Taichung, Taiwan.
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DL Poly - A parallel molecular dynamics simulation package.
Meta Description: [ The Molecular Simulation Group of
CLRC, UK seeks to promote leading edge research in molecular
simulation in the UK through development and exploitation of advanced
software on high perfomance computers ]
EGO - A parallel program for molecular dynamics simulations of biomolecules.
EGO VIII - A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
Meta Description: [ EGO - A Program for Efficient Parallel Molecular Dynamics ]
Folding@home - It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
Genoscience - Genmol is a 3D molecular modeling software for measuring resistance/affinity between a ligand and a target, used for disease management and drug discovery. Details of company in Marseille, France.
Meta Description: [ Genoscience is a biopharmaceutical company focus on the development of new drugs against viruses such as Hepatitis C HCV. The company develops three families of compounds: HCV protease inhibitors, HCV fusion inhibitors ]
Ghemical - An easy-to-use molecular editor and modeling package with all-atoms molecular mechanics, reduced protein models and links to many common chemistry programs. Ghemical is released under the GNU GPL and includes source code.
GROMOS - A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
Meta Description: [ ETH Zuerich ]
Helical Wheels - Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
Highlights of Biochemistry - Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany.
Meta Description: [ Universität Hamburg, Biocenter Klein Flottbek, Ohnhorststr. 18 ]
IMB Jena Image Library of Biological Macromolecules - Resource for visualization and analysis of 3D-biopolymer structures; proteins, nucleic acids, carbohydrates, and small molecule ligands. Combines experimental and computer generated models, maintained in Germany.
Meta Description: [ JenaLib Home, An introduction to structural biology and an interface to the structure databases NDB and PDB with lots of images and an interactive viewer ]
Jay Ponder Lab - Graphical user interface to suites of molecular modeling tools, providing an integrated environment for engineering applications. Contacts for the group at Washington University School of Medicine in Saint Louis, Missouri.
Meta Description: [ Jay Ponder Lab Home Page ]
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NAMD - A parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.
Pande Group - Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
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Protein Dynamics, Inc. - Molecular dynamics simulation programs for proteins, DNA, and RNA, including 3D viewing of molecules. Offers downloadable demonstration version, from Milpitas California.
Protein Structure Database - PSdb uses primary data, to relate secondary and tertiary information, for solvent accessibility, internal relative distances, and ligand interactions. Maintained at the Mellon Institute, Pittsburgh, Pennsylvania.
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RAFT - Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
RAMP - Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix.
Sesame Project - Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
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Southwest Biotechnology and Informatics Center - Sequence analysis tools including protein classification with the assistance of predicted secondary structure and sequence format tools, available under license from New Mexico State University.
Meta Description: [ SWBIC provides a single-point access to a vast store of widely distributed biotechnology information as well as developing new educational and bioinformatics services. ]
SWISS-MODEL - SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
TINKER - A free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers. Distributed as source code and as binaries for Windows9x, Linux and Mac.
WhatIf - Protein structure analysis software for Linux, SGI/IRIX, Windows NT. Performs mutant prediction, structure verification, homology modeling and molecular visualization. Links to the documentation in HTML. Commercial software.
X-plor Archives - Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington.
YASARA - (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
ZMM Software Inc. - Modeling tool for theoretical studies, employing molecular mechanics approach in combination with Monte Carlo energy minimization algorithm. Downloads on secure server, and contacts in Flamborough, Ontario.
Meta Description: [ Easy to use molecular modeling program ]
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