Insight works only on the SGI workstations, Loop, Turn, Coil in Beckman 050C.
Open a Unix Shell using the pull down menu on the SGI Desktop Icon. Type insightII
A copy of the InsightII training manual is in the Molecular Modeling Lab. You may borrow it to make a copy for your self. Please return one of the copies so others may do the same.
Insight does have an excellent tutorial built into the software. Click on the little icon at the bottom left of the screen that looks like a moarter-board hat.
The Insight On-Line manual is also available using your Web browser. Also, check out the MSI Web pages on InsightII
Modules We Have What it Does Creates, modifies, manipulates, displays, and analyzes
molecular systems and related data and provides the core
requirements for all Insight II software modules Apex-3D Is a powerful and flexible program for high-level
analysis of molecular structure and the results of molecular
dynamics simulations. A unique package for computer-assisted assignment of 2D,
3D, and 4D NMR spectra of proteins and nucleic acids, which
includes tools for semiautomatic spin system detection,
identification, sequential assignment, and NOE crosspeak
assignment. An option of the FELIX program that provides direct
interaction between experimental NOESY data, molecular
structures, and back-calculated NOESY data within an
integrated interface. FELIX is the industry standard for off-line data
processing, spectral visualization and analysis software
for all types of high resolution, one-dimensional to
four-dimensional, homonuclear and heteronuclear NMR data.
FELIX is built upon the foundations of a relational
database, an extensive macro language, and an easy-to-use,
multi-windowed, menu-driven interface allowing quick and
easy performance of routine tasks. Felix-X-Remote 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 is a powerful tool for de novo rational drug design. Ludi
can be used to fit molecules into the active site of a
receptor by identifying and matching complementary polar and
hydrophobic groups. NMR Refine Advanced Expands the refinement capabilities found in NMR
Refine/DG-II to include simulated annealing and restrained
molecular mechanics and dynamics (MD Schedule), refinement
of NOE intensities using hybrid-matrix approaches (IRMA),
direct refinement of NOE volumes (NOE-MD), an interface to
back-calculating 2D NOESY crosspeak intensities (NOE
Simulate), and a spreadsheet method of analyzing NMR-related
structural and dynamical molecular parameters (Query). NMR Refine DGII Provides an entry-level option into NMR refinement
software with capabilities for generating structures from
NMR-derived distance and dihedral restraints. The DG-II,
Restraint Analysis, NMR Database and ProStat pulldowns
combine to give the NMR spectroscopist the necessary tools
for generating, analyzing and verifying high resolution
structures. Open Interface A patented technology exclusively licensed to MSI, uses
"environmental classification" of protein residues to assess
whether a primary sequence is compatible with the current 3D
structural model. Profiles-3D is used to search a
structural-motif database with a new sequence, looking for
compatibility; search a sequence database with an example
stucture, seeking similarity; or verify the agreement
between the sequence and current model of a protein
sequence/structure under study. Generates and compares the conformations of different
molecules. You can operate on molecular fields and volumes,
superimpose two or more molecules, and search systematically
for sterically allowed conformations Is used to draw molecules in 2D and automatically convert
them to 3D models. Constructs models of peptides, proteins, carbohydrates,
and nucleic acids for visualizing complex macromolecular
structures and for use in further simulation work. 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. 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 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. QuanteMM Combines quantum mechanical and force field methods,
allowing you to use accurate first-principles methods to
study cluster models while taking the surrounding
environment fully into account. Large and complex systems
can be studied with high accuracy. Converter Builds 3D models from 2D structural database output 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 MODELER uses a new comparative modeling methodology to
rapidly build structural models for protein sequences
without a known structure. MODELER's unique methodology builds a structure by
simultaneously satisfying spatial restraints and local
molecular geometry. Structural models for a sequence can be
constructed from structures of one or more homologous
proteins in the same family. With about one third of known
sequences related by homology to one or more known
structures, homology modeling can provide useful models ,
which guide biochemical experiments far beyond the range of
experimentally determined structures. In addition, these
models can speed the process of experimental structure
determination by molecular replacement phasing in X-ray
crystallography and NOE assignment in NMR structure
determination. And as more and more structures are
experimentally determined, homology models can be
constructed for an increasing variety of sequences. CHARMm (Chemistry at HARvard Macromolecular Mechanics) is
a highly regarded and widely used simulation package. CHARMm
combines standard minimization and dynamics capabilities
with expert features including normal mode calculations,
correlation analysis, and combined quantum and molecular
mechanics (QM/MM) methods. Simulations provide information
concerning molecular-level structure, interactions, and
energetics. This program allows you to perform classical
empirical energy calculations on a variety of small and
large molecular systems, including proteins, nucleic acids,
and carbohydrates. Using the latest algorithms and
methodology, you can explore in detail the dynamics and
thermodynamics of your system of interest, providing insight
into your current experiments and suggesting new directions
for future efforts. Binding Site Analysis combines several tools that enable
you to identify and characterize a protein's binding site
and then use those characteristics to look for similar
features in other proteins of known structure. SeqFold provides a new algorithm developed in the
laboratory of Professor David Eisenberg(1-3), which aids in
the functional identification of proteins. Using an approach
based on fold recognition, SeqFold helps you to identify
homologous proteins when traditional sequence searching
methods fail.
Modules We Don't Have What it Does Catalyst Modeling, hypothesis generation and structure search for
drug discovery Cerius2 Simulation environment for life and materials science Ceriius2 SDK Tools for scientific software development Quanta Specialist modeling tools for macromolecules and small
organics WebLab Computational science on the WWW Solids Builder and other Solids modeling constructs models of inorganic and organic crystals,
metals, layers, and interfaces, which are used to develop
and validate models of solids and surfaces Synthia estimates polymer properties using statistically-derived
correlations. You can predict properties quickly from
existing data for a broader range of polymers than
conventional QSPR methods. ESOCS calculates the electronic and magnetic properties of
solids. You can efficiently compute quanities such as the
electronic structure of defects, optical absorption and
reflection spectra, and magnetic properties of materials.
ESOCS has wide application to metals and alloys, the pigment
industry, and for optimizating and designing magnetic
materials such as in the disc drive industry Interfaces calculates the conformational properties of polymers in
the vicinity of an interface MADSYS is a program that provides phasing of multi-wavelength
anomalous dispersion (MAD) data collected at synchrotron
radiation X-ray sources. Miscibility is a navigational aid for predicting liquid-liquid phase
diagrams of polymer solutions or blends. It increases your
productivity by unifying MSI's tools for phase diagram
prediction and leading you through appropriate simulation
strategies Phase Diagram calculates liquid-liquid phase diagrams for polymer
solutions and blends, helping you to optimize the properties
of formulations. Plane Wave is a quantum mechanics module for the materials sciences.
You can simulate solids, interfaces, and surfaces for a wide
range of materials classes including ceramics and
semiconductors, determining properties such as geometric
structure, energies, band-structures, and charge
density. Polymizer builds 3D models of linear and branched homopolymers and
copolymers, enabling you to visualize and simulate polymer
structure and behavior. PRISM predicts polymer blend miscibility and related properties
based on the chemical composition of the chains in the
blend. PRISM helps you relate chemistry to properties for
improved formulation design. QSPR estimates the properties of a wide range of thermoplastic
materials using group additivity methods. QSPR provides you
with rapid predictions and maximizes your use of existing
experimental data. RIS rapidly calculates the conformational properties of
polymer chains, which helps you relate these to their
chemical structure. Fast Structure allows you to determine equilibrium geometries of
crystals, interfaces, surfaces and molecules. It calculates
structures using fast first-principles density functional
methods in conjunction with molecular dynamics, simulated
annealing and minimization techniques. FastStructure is used
in the electronics, chemicals, petrochemicals, and glass
industries. CFF an advanced Class II force field, is used to optimize
DNA, RNA, carbohydrates, lipids, proteins, peptides, and
small-molecule models, giving a high confidence level for
calculations in drug discovery, protein design, genomic
theraputics, NMR spectroscopy, and X-ray crystallography Amorphous Cell constructs and analyzes models of bulk amorphous systems
such as polymers and glasses. You can investigate properties
such as cohesive energy, chain dimensions, chain packing,
and local dynamical behavior Characterize simulates, displays, and interprets a wide variety of
analytical data. It is used to process HRTEM, NMR,
diffraction, IR Raman, EXAFS, and Morphology data. ZINDO s a semi-empirical molecular-orbital program for studying
the spectroscopic properties of molecules and complexes.
ZINDO can be applied to a wide range of compounds, including
organic and inorganic molecules, polymers, and
organometallic complexes.
Connelly surfaces and enhanced structure displays are available in Insight through the Molecule/connelly pull down menu.
Use the merge function to make one logical object
You may get PDB files from the Brookhaven Protein Data Bank, or from the /PDB directory on your machine. The /PDB files are compressed, so InsightII requires that you uncompress them first.