InsightII

InsightII is a molecular modeling package consisting of several programs, including Insight II, BioPolymer, Analysis, Discover. InsightII is a comprehensive graphic molecular modeling program. Used in conjunction with the molecular mechanics/dynamics program Discover, InsightII can be used to build and manipulate virtually any class of molecule or molecule system. Molecular properties can be studied through InsightII's interface with other Biosym products such as DelPhi, DMol, and Discover.

The following modules are available to researchers:

Package	Concurrent Users	Description (from the Molecular Simulations/Biosym web site)
Insight II	10	Insight creates, modifies, manipulates, displays, and analyzes molecular systems and related data and provides the core requirements for all Insight II software modules.
Affinity	1	Affinity is a suite of programs for automatically docking ligand to a receptor. Specifically, for a given assembly consisting of a ligand molecule and a receptor molecule.
Analysis	12	Analysis revolves around mathematical and geometric modeling of molecular properties. It is a software program that allows users to abstract molecular properties dynamically from molecular structures and simulations. Analysis is a "dynamic molecular information system". Molecular properties are defined interactively, evaluated dynamically, and visualized interactively through dynamically linked spreadsheets, 2D and 3D graphs, and 3D molecular graphics representations.
Biopolymer	8	Biopolymer constructs models of peptides, proteins, carbohydrates, and nucleic acids for visualizing complex macromolecular structures and for use in further simulation work.
CHARMM	2	CHARMM is a simulation program available within insightII. CHARMm uses empirical energy functions to describe the forces on atoms in molecules. These functions, plus the parameters for thei functions, constitute the CHARMm force field. Well-validated energy and force calculations form the core of a broad range of calculation and simulation capabilities, including calculation of interaction and conformational energies, local minima, barriers to rotation, time-dependent dynamic behavior, free energy, and vibrational frequencies.
Consensus	1	Consensus builds a 3D model of a protein from its amino acid sequence and the known structures of related proteins using distance constraints derived from the reference protein structures.
Converter	4	Converter automatically generates 3D molecules from a database containing 2D representations of molecular structures. It reads 2 D information from the MOL and SD files produced with Molecular Design, Ltd. (MDL) software and outputs 3D structures that are fully compatible with the IsightII and MDL software.
DeCipher	1	DeCipher's philosophy revolves around mathematical and geometric modeling of molecular properties. It is a software program that allows users to abstract molecular properties dynamically from molecular structures and simulations. DeCipher is a "dynamic molecular information system". Molecular properties are defined interactively, evaluated dynamically, and visualized interactively through dynamically linked spreadsheets, 2D and 3D graphs, and 3D molecular graphics representations.
Delphi	4	DelPhi calculates electrostatic potentials and solvation energies of both large and small molecules, including nucleic acids. You can use DelPhi to rigorously examine the effects of charge distribution, ionic strength, and dielectric constant on the electrostatic potentials of macromolecules.
Discover and Discover3	10	Discover is a simulation program available within Insight II. It incorporates a range of well validated forcefields for dynamics simulations, minimization, and conformational searches, allowing you to predict the structure, energetics and properties of organic, inorganic, organometallic, and biological systems. Discover also implements IPC (Inter Process Communications), which allows users to instruct Discover to turn processing control over to external programs, and retrieve the results of those external processes, incorporating them into the continuing Discover computations.
Homology	2	Homology builds a 3D model of a protein from its amino acid sequence and the known structure of related proteins. Standard techniques of backbone building, loop modeling, structural overlay and statistical analysis of the resulting models are available.
Ludi	1	The Ludi program runs in both receptor and active analogue mode. It allows user to design de nove candidate ligands for the active sites of proteins, suggest modifications of known ligands, manage libraries of candidate fragments, and scores ligand-complex complexes.
Modeler	3	Modeler is an automated homology modeling scheme designed to find the most probable three dimensional structure of a protein, given its amino acid sequence and its alignment with related structures. It derives 3D protein models without the time consuming separate stages of core region identification and loop region building or searching that are inherent to manual homology modeling schemes.
NMR Refine	3	NMR_Refine is dedicated to structure generation and refinement. This module contains the tools necessary for constructing a comprehensive NMR database; generating an approximate molecule structure using simulated annealing or distance geometry; further refining the structure with the iterative relaxation matrix approach (IRMA) and direct NOE methods; and evaluating the structures obtained at each step of the process, enabling their accuracy and precision to be assessed. NMR_Refine also provides restraint analysis. NMR_Refine uses the programs DGII, IRMA, Discover, and X-PLOR to perform these various tasks.
Search_Compare	1	The Search_Compare module contains the pulldown Volume, Overlap, SC_Search, Vector_Map, Conformer, Distance_Map, Spreadsheet, Graph and Background_Job. The commands in Search_Compare enable users to calculate and operate on molecular volumes, to superimpose two or more molecules, to search systematically for sterically allowed conformations of a molecule and to quickly find and examine conformations of interest after they have been generated.

To run insightII, you must first set some environment varibles. This is easy. Just type

source /usr/local/accelrys/accelrys.csh

Now type

insightII

Version: 2000.1
Labs:Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab, Computational Genetics Laboratory
System(s): all SGI workstations
Categories: Molecular Modeling, X-ray Crystallography, Molecular Simulation

For more information, see http://www.msi.umn.edu/software/biosym/tutorial/index.html.