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Internal Coordinate Mechanics (ICM) is a software program and algorithm to predict low-energy conformations of molecules by sampling the space of internal coordinates (bond lengths, bond angles and dihedral angles) defining molecular geometry. In ICM each molecule is constructed as a tree from an entry atom 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 substrates and coenzymes.[1]
Software
ICM also is a programming environment for various tasks in computational chemistry and computational structural biology, sequence analysis and rational drug design. The original goal was to develop algorithms for energy optimization of several biopolymers with respect to an arbitrary subset of internal coordinates 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 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
Bai, Shuju; Du, Tianchuan; Khosravi, Ebrahim (October 2010). "Applying internal coordinate mechanics to model the interactions between 8R-lipoxygenase and its substrate". BMC Bioinformatics. 11 (S6): S2. doi:10.1186/1471-2105-11-S6-S2. PMC 3026367.
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. PMID 8289329
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. doi:10.1002/jcc.540150503
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. doi:10.1002/jcc.540151006
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) Archived 2017-07-02 at the Wayback Machine (ICM supports electron density visualization)
vte
Computational chemistry software
Cheminformatics
Free software
Avalon Cheminformatics Toolkit Bioclipse Blue Obelisk Chemistry Development Kit ECCE JOELib OELib Open Babel RDKit
Proprietary
Canvas Chemicalize Discovery Studio
Chemical kinetics
Free software
APBS Cantera KPP
Proprietary
Autochem Chemical WorkBench CHEMKIN COSILAB DelPhi Khimera
Molecular modelling
and
visualization
List of molecular graphics systems
Free software
Ascalaph Designer Avogadro BALL Biskit Gabedit Ghemical Jmol Molekel PyMOL QuteMol RasMol
Proprietary
Abalone ACD/ChemSketch Atomistix ToolKit ChemDraw ChemWindow EzMol Gaussian Maestro MarvinSketch MarvinView MODELLER Molecular Operating Environment SAMSON Spartan UCSF Chimera VMD
Molecular docking
List of protein-ligand docking software
Free software
AutoDock AutoDock Vina FlexAID rDock
Proprietary
Glide LeDock Molecular Operating Environment
Molecular dynamics
Free software
CP2K GROMACS LAMMPS OpenMM PLUMED
Proprietary
Abalone AMBER CHARMM CPMD Desmond GROMOS NAMD
Quantum chemistry
List of quantum chemistry and solid-state physics software
Free software
ABINIT ACES (CFOUR) AIMAll BigDFT COLUMBUS CONQUEST CP2K Dalton DIRAC DP code FLEUR FreeON MADNESS MPQC NWChem Octopus OpenMolcas PARSEC PSI PyQuante PySCF Quantum ESPRESSO (PWscf) RMG SIESTA VB2000 YAMBO code
Proprietary
ADF AMPAC DMol3 CADPAC CASINO CASTEP CPMD CRUNCH CRYSTAL Firefly GAMESS (UK) GAMESS (US) Gaussian Jaguar MOLCAS MOLPRO MOPAC ONETEP OpenAtom ORCA PLATO PQS Q-Chem Quantemol Scigress Spartan TeraChem TURBOMOLE VASP WIEN2k XMVB
Skeletal structure drawing
Free software
JChemPaint Molsketch XDrawChem
Proprietary
ACD/ChemSketch BIOVIA Draw ChemDoodle ChemDraw ChemWindow JME Molecule Editor MarvinSketch
Others
Aqion Eulim EXC code GenX GSim Mercury CrystalExplorer ICM (ICM-Browser) Materials Studio Molden OpenChrom SASHIMI
Hellenica World - Scientific Library
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