Internal Coordinate Mechanics (ICM) is a software program and algorithm to predict low-energy conformations of

molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bio ...

s by sampling the space of internal coordinates (

bond length In molecular geometry, bond length or bond distance is defined as the average distance between nuclei of two bonded atoms in a molecule. It is a transferable property of a bond between atoms of fixed types, relatively independent of the rest ...

s, bond angles and dihedral angles) defining

molecular geometry Molecular geometry is the three-dimensional space, three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometric ...

. In ICM each molecule is constructed as a tree from an entry

atom Every atom is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Only the most common variety of hydrogen has no neutrons. Every solid, liquid, gas ...

where each next atom is built iteratively from the preceding three atoms via three internal variables. The rings kept rigid or imposed via additional restraints. ICM is used for modelling peptides and interactions with

substrate Substrate may refer to: Physical layers *Substrate (biology), the natural environment in which an organism lives, or the surface or medium on which an organism grows or is attached ** Substrate (locomotion), the surface over which an organism lo ...

s and

coenzyme A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's role as a catalyst (a catalyst is a substance that increases the rate of a chemical reaction). Cofactors can be considered "helper molecules" that ass ...

Software

ICM also is a programming environment for various tasks in

computational chemistry Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of mo ...

and computational

structural biology Structural biology is a field that is many centuries old which, and as defined by the Journal of Structural Biology, deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every le ...

sequence analysis In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Methodologies used include sequence align ...

and rational

drug design Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that ac ...

. The original goal was to develop algorithms for energy optimization of several

biopolymer Biopolymers are natural polymers produced by the cells of living organisms. Like other polymers, biopolymers consist of monomeric units that are covalently bonded in chains to form larger molecules. There are three main classes of biopolymers ...

s with respect to an arbitrary subset of

internal coordinates In chemistry, the Z-matrix is a way to represent a system built of atoms. A Z-matrix is also known as an internal coordinate representation. It provides a description of each atom in a molecule in terms of its atomic number, bond length, bond ...

such as bond lengths, bond angles torsion angles and phase angles. The efficient and general global optimization method which evolved from the original ICM method is still the central piece of the program. It is this basic algorithm which is used for peptide prediction,

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 p ...

and loop simulations, flexible macromolecular docking and energy refinement. However the complexity of problems related to structure prediction and analysis, as well as the desire for perfection, compactness and consistency, led to the program's expansion into neighboring areas such as graphics, chemistry, sequence analysis and database searches, mathematics, statistics and plotting. The original meaning became too narrow, but the name was kept. The current integrated ICM shell contains hundreds of variables, functions, commands, database and web tools, novel algorithms for structure prediction and analysis into a powerful, yet compact program which is still called ICM. The seven principal areas are centered on a general core of shell-language and data analysis and visualization.

References

* Abagyan, R.A. and Totrov, M.M. ''Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations For Peptides and Proteins'' J. Mol. Biol., ''235'', 983–1002, 1994. * Abagyan, R.A., Totrov, M.M., and Kuznetsov, D.A. ''ICM: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation''. J. Comput. Chem., ''15'', 488–506, 1994. *Totrov, M.M. and Abagyan, R.A. ''Efficient Parallelization of The Energy, Surface and Derivative Calculations For internal Coordinate Mechanics''. J. Comput. Chem., ''15'', 1105–1112, 1994.

External links

The NERF algorithm for efficient conversion of sequential torsion angles to Cartesian coordinates

www.molsoft.com

iSee (interactive Structurally enhanced experience)

EDS (Electron Density Server)
(ICM supports electron density visualization) {{Chemistry software Computational chemistry software