MODELLER
Encyclopedia
MODELLER is a computer program
used in producing homology models
of protein
tertiary structure
s as well as quaternary structure
s (rarer). It implements a technique inspired by nuclear magnetic resonance known as satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability density function
for the location of each atom
in the protein. The method relies on an input sequence alignment
between the target amino acid
sequence to be modeled and a template protein whose structure has been solved.
The program also incorporates limited functionality for ab initio structure prediction of loop regions of proteins, which are often highly variable even among homologous
proteins and therefore difficult to predict by homology modeling.
MODELLER was originally written and is currently maintained by Andrej Sali
at the University of California, San Francisco
. Although it is freely available for academic use, graphical user interface
s and commercial versions are distributed by Accelrys
. A freely available GUI to MODELLER called EasyModeller is developed by Kuntal Kumar Bhusan at University Of Hyderabad,India. A new version of EasyModeller (EasyModeller 2.0) has been recently released and available for free download. There is also a simple interface to MODELLER in the program UCSF Chimera
.
Computer program
A computer program is a sequence of instructions written to perform a specified task with a computer. A computer requires programs to function, typically executing the program's instructions in a central processor. The program has an executable form that the computer can use directly to execute...
used in producing homology models
Homology modeling
Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein...
of protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
tertiary structure
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
s as well as quaternary structure
Quaternary structure
In biochemistry, quaternary structure is the arrangement of multiple folded protein or coiling protein molecules in a multi-subunit complex.-Description and examples:...
s (rarer). It implements a technique inspired by nuclear magnetic resonance known as satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability density function
Probability density function
In probability theory, a probability density function , or density of a continuous random variable is a function that describes the relative likelihood for this random variable to occur at a given point. The probability for the random variable to fall within a particular region is given by the...
for the location of each atom
Atom
The atom is a basic unit of matter that consists of a dense central nucleus surrounded by a cloud of negatively charged electrons. The atomic nucleus contains a mix of positively charged protons and electrically neutral neutrons...
in the protein. The method relies on an input sequence alignment
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
between the target amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
sequence to be modeled and a template protein whose structure has been solved.
The program also incorporates limited functionality for ab initio structure prediction of loop regions of proteins, which are often highly variable even among homologous
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
proteins and therefore difficult to predict by homology modeling.
MODELLER was originally written and is currently maintained by Andrej Sali
Andrej Šali
Andrej Šali is a computational structural biologist. He joined the faculty of the Rockefeller University in 1995, following his postdoctoral research at Harvard University...
at the University of California, San Francisco
University of California, San Francisco
The University of California, San Francisco is one of the world's leading centers of health sciences research, patient care, and education. UCSF's medical, pharmacy, dentistry, nursing, and graduate schools are among the top health science professional schools in the world...
. Although it is freely available for academic use, graphical user interface
Graphical user interface
In computing, a graphical user interface is a type of user interface that allows users to interact with electronic devices with images rather than text commands. GUIs can be used in computers, hand-held devices such as MP3 players, portable media players or gaming devices, household appliances and...
s and commercial versions are distributed by Accelrys
Accelrys
Accelrys is a software company headquartered in the US, with representation in Europe and Japan. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries.Accelrys started in 2001...
. A freely available GUI to MODELLER called EasyModeller is developed by Kuntal Kumar Bhusan at University Of Hyderabad,India. A new version of EasyModeller (EasyModeller 2.0) has been recently released and available for free download. There is also a simple interface to MODELLER in the program UCSF Chimera
UCSF Chimera
UCSF Chimera is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality and can be created...
.