Life Science Software

Showing posts with label Molecular modeling software. Show all posts

ChemBioDraw - Molecular Modeling Software

ChemBioDraw is the sole chemical and biological drawing suite required for the serious life science professional, containing advanced prediction tools and full Web integration using the ChemBioDraw ActiveX/Plugin. Features include proton NMR with peak splitting and highlighting, amino acid and DNA sequence tools, TLC plate drawing tool, Struct=Name, ISIS/Draw mode and stoichiometric analysis.

Software Link: ChemBioDraw - Molecular Modeling Software

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ChemBio3D brings workstation-quality molecular graphics and rigorous computational methods to your desktop. Integration with molecular analysis makes ChemBio3D the ideal software for chemists and biochemists. The ChemBio3D software suite also includes ChemDraw, ChemFinder, and E-Notebook. Features include state-of-the-art protein visualization, open GL graphics and stereo glasses, molecular mechanics and semi-empirical calculations with interfaces to MOPAC, Jaguar GAMESS and Gaussian.

Software Link : Molecular Modeling Software

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BioLego is an interactive modeling and simulation platform built on Strand's award winning AVADIS® technology.

With BioLego you can:

Build Your Own Models
Access, modify and customize dynamic systems models built at Strand
Generate and/or Test Hypothesis in silico
Visualize, Store, Retrieve and Compare Results

BioLego features include:

Transparent and comprehensive knowledge-base
In BioLego you can annotate each model in detail and view all model components such as differential equations, kinetic expressions, parameters, alongwith their values and units, thus ensuring complete transparency. BioLego handles a large number of literature references with direct links to PubMed thus contributing to the building of an exhaustive and model specific knowledge-base.

Handling Complexity
In BioLego, you can visualize a complex mathematical model as an intuitive, information-rich and interactive network of biological interactions. Complicated and interconnected networks can be visually simplified to enhance biological understanding while retaining all the complexity of the interconnectedness.

Reliable solvers
BioLego is powered by a set of robust solvers that ensure reliable results for each simulation. A variety of stiff solvers are available to handle large variations in time-scales typical of complex biological systems.

Large scale data handling and sharing
BioLego supports user management of large numbers of experiments with the ability to quickly store retrieve, visualize and compare results. BioLego facilitates easily sharing of projects and data with other users both in Desktop and Enterprise versions.

Software Link: BioLego - Modeling and simulation Software

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Interactive 3D Molecular Graphics with ChemSite Pro®
Comprehensive Molecular Modeling Program Enables Users to Build Any Chemical Structure Quickly and Professionally

ChemSite Pro is an interactive 3D molecular graphics environment that enables the chemist to build, study, and present molecules in an impressive visual environment. The intuitive Windows interface makes ChemSite Pro easy to learn and use. Interactive 3D modeling and real time animation lets you use molecular building blocks or atom by atom construction to visualize even the most complex structures.

This versatile molecular modeling program enables users to draw, display, and simulate the dynamic behavior of protein, DNA, organic, and inorganic molecules as fully realized, space-filling entities. ChemSite Pro comes with a fully interactive crystal builder, enabling ionic, metallic, covalent and molecular crystals to be constructed from a database of all 230 space groups.

ChemSite Pro also makes it easy to build molecules by sketching them as you would on paper and then automatically convert the sketch to an accurate 3D model. You can even create and playback molecular dynamics. Photo-realistic rendering tools such as Bezier curves, Ray tracing, Phong shading and texture-mapped atom symbols help create stunning presentations.

ChemSite Pro images can be exported to other Windows applications with a single mouse click. The program works interactively with CISPro, MMP+ and NIST Mass Spec Search programs.

Powerful analysis features include tools and techniques formerly found only on workstation level modeling programs. The program delivers full support for stereo chemistry, for example, with dashes and wedges around chiral centers and auto-determination of R and S stereo centers. Files can be freely imported and exported in all the most popular formats including Brookhaven, ChemDraw connectivity table, and Mopac Z-matrix.

An extensive library of organic molecules suitable for college organic chemistry courses is included for use with lessons from popular organic chemistry textbooks, such as McMurray, making it a great teaching tool! The latest version displays molecular surfaces calculated with semi-empirical quantum mechanics and provides improved graphic performance. Easily draw any 2D structure for publication-quality graphics and automatically convert to 3D modeling.

Versatile Molecular Modeling and Simulation

Build lipids and lipid bilayers
Build synthetic polymers
Build lipid bilayers and perform MD simulation in water under 2D periodic boundary conditions
Perform semi-empirical extended huckel calculations
Performs Ab Initio, MP2 and DFT Calculations: includes all the popular basis sets from STO-3G to 6-311G**
Build crystals based on all of the 230 space groups
Calculate and display molecular orbitals: total electron density and frontier orbitals (HOMO, LUMO)
Display electron spin density
Display the electrostatic potential
Calculates Ab Initio, DFT, del Re, Huckel and Extended Huckel atomic charges
Works interactively with CISPro, MMP+ and NIST Mass Spec Search programs
New implicit solvent models for molecular dynamics

Software Link : ChemSite Pro - Molecular Modeling Software

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The Mathematica biological sciences solution offers a complete workflow-from data import to high powered analysis through automatic report generation and interactive deployment-all in one system, with no need for programming.

Curated genome and protein data are built into Mathematica alongside highly automated computation for ease and accuracy of calculations.

Mathematica includes thousands of built-in functions for computation, modeling, visualization, development, and deployment »

Biological sciences specific capabilities:
Free-form linguistic input produces immediate results without the need for syntax »
Built-in genomic, proteomic, and chemical data, ready for use without preprocessing »
Ready-to-use built-in functions for all standard statistical and data analysis techniques-such as principal component analysis, nonlinear regression, analysis of variance, and more-for applications in ecology, molecular biology, and other areas »
Drag and drop images into your notebook and apply image processing techniques to study macromolecular structures, bone cross-section features, computer-aided cell analysis, and much more »
Build interactive applications with a single command to prototype models, such as a network design for controlling virus spread, and study the effects of changing parameters »
Instantly generate reports and interactive applications, and share them with other biologists or colleagues using Wolfram CDF Player »
Easily create standardized or highly customized publication-quality graphics using built-in functions »
Highly automated differential equation solvers analyze your equations and select the right algorithms to get you accurate answers quickly for applications in ecology, molecular dynamics, and more »
Import and export data in many biomolecular formats, including Affymetrix, PDB, MMCIF, GenBank, and FASTA »
Extensive and easy-to-use linking and connectivity capabilities to databases and Java, C, and .NET codes »
Complete integrated platform for modeling biological systems, analyzing data, interactively visualizing results, and generating automatic lab reports

Built-in biological sciences data immediately suitable for computation
Genome Data »
Integrated curated data on the entire DNA sequence of the human genome
Protein Data »
Built-in data on all reference human proteins
Chemical Data »
Detailed physical, chemical, and molecular properties of more than 34,000 compounds

Software Link: Mathematica biological sciences solution - Molecular Modeling Software

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Chemical Reaction and Equilibrium Software HSC Chemistry is the world's favorite thermochemical software with a versatile flowsheet simulation module. HSC is designed for various kinds of chemical reactions and equilibria calculations as well as process simulation.

The current HSC version 7.0 contains 22 calculation modules:

1. Sim - Process simulation
2. Reactions Equations
3. Heat and Material Balances
4. Heat Loss Calculator
5. Equilibrium Calculations
6. Electrochemical Cell Equilibriums
7. Eh-pH Diagrams - Pourbaix
8. H, S, C and Ellingham Diagrams
9. Tpp Diagrams - Stability diagrams
10. Lpp Diagrams - Stability diagrams
11. Water - Steam tables, etc.
12. H, S, Cp Estimates
13. Conversions - Species to elements
14. Mineralogy Iterations
15. Periodic Chart - Elements
16. Measure Units
17. HSC AddIn Functions
18. Data - Statistical analysis
19. Geo - Mineralogical calculations
20. Map - GPS material stock
21. Fit - Numerical Data fit
22. Aqua

The name of the program is based on the feature that calculation modules automatically utilize the same extensive thermochemical database which contains enthalpy (H) , entropy (S) and heat capacity (C) data for more than 25 000 chemical compounds. This database is equivalent to more than twenty thick data books. HSC contains also other databases:

1. H, S and Cp Thermochemical Database
2. Water Steam/Fluid Database
3. Heat Conduction Database
4. Heat Convection Database
5. Surface Radiation Database
6. Gas Radiation Calculator
7. Particle Radiation Calculator
8. Elements Database
9. Measure Units Database
10. Minerals Database with 3581 minerals
11. Aqueous Solution Density Database
12. The Pitzer parameter database

The objective of HSC is to make conventional thermodynamic calculations fast and easy to carry out using personal computers. Therefore HSC has a wide range of applications in scientific education, industry and research. Thermochemical calculations are useful, for example, when developing new chemical processes and improving old ones. HSC Chemistry is also a useful tool for universities and schools in chemical practicals and studies.

Traditionally, thermodynamic calculations based on experimental or assessed data have utilized stability functions in various thermodynamic data books and papers in scientific journals. The difficult searching stage and complicated calculations, as well as inconsistencies arising from different selections of standard and reference states, have made this calculation procedure quite time-consuming.

HSC Chemistry offers powerful calculation methods for studying the effects of different variables on the chemical system at equilibrium. For example, if the user gives the raw materials, amounts and other conditions of almost any chemical process, the program will give the amounts of the product as a result. HSC also makes heat and material balance calculations of different processes much more easily than any manual method. The Eh-pH-diagrams option also offers a very fast way of studying the dissolution and corrosion behavior of different materials.

Of course, HSC cannot solve all chemical problems, because it does not take into account the kinetics (rates) of the chemical reactions and non-ideality of solutions. However, in many cases it is a very inexpensive and useful tool which helps to find the optimal reaction conditions and yields for experimental investigations without expensive trial-and-error chemistry.

Software Link : HSC Chemistry - Chemical Reaction and Equilibrium Software

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Comprehensive 3-D Molecular Visualization and Rendering Software

ChemSite is a three-dimensional (3-D) molecular modeling program for drawing, displaying, and simulating the dynamic behavior of organic and biological molecules. The program offers an interactive molecule building facility for the creation of almost any molecule. Biological macromolecules can be built by hand or imported from Brookhaven Protein Data Bank files. ChemSite also reads and writes data files from other molecular modeling and chemical drawing programs, including Molecular Design Limited (MDL) .mol files, Mopac Z-matrix files, and cartesian A files.

Molecules can be rotated in 3-D in real time, and a variety of sophisticated rendering techniques are available for visualizing molecules as space-filling entities. Photorealistic graphics can be generated with ChemSite on PCs equipped with a Super VGA graphics adapter. And ChemSite now allows new implicit solvent models for molecular dynamics.

Since molecules are not static and can adopt a multitude of conformations or shapes, visualization of conformational flexibility is vital to understanding molecular structure and function. The flexible nature of molecules can be studied with ChemSite's molecular dynamics facility. Energy minimization, constant-temperature, and constant-energy molecular dynamics simulations can be conducted with any molecule or system of molecules, and dynamics trajectories, including conformational patterns and behavior, can be saved for playback at a later time.

ChemSite is an inexpensive and easy-to-use alternative for generating 3-D representations of molecular structures and performing basic molecular modeling. Students new to the world of chemistry will benefit from the visual environment for studying the nature of molecules and from ChemSite's built-in rules of chemistry. Educators can use ChemSite to illustrate concepts in lecture presentations and course materials. Researchers in academia and industry will find ChemSite useful for advanced studies of structures and easy development of detailed models for papers and presentations.

Software Link: ChemSite - Molecular Modeling Software

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Superior Molecular Modeling Capabilities in a Single, Affordable Application

MolSuite gives you molecular modeling with great graphics, physical property calculations, statistical analysis, and database development and management all in one complete package.

Model building is easy in ChemSite Pro which provides fast minimization and displaying of any molecule, even crystals, in a 3D environment. Structures are easily copied and pasted to other MolSuite programs. Paste your molecule into Molecular Modeling Pro Plus and run semi-empirical quantum mechanics and calculate up to 70 properties. Molecular Modeling Pro Plus enables you to use statistical regression techniques used in the plotting of chemical data.

Use MolSuite to develop and maintain your own molecular modeling database or use MolSuite DB, which contains over 24,000 organic molecules with chemical properties.

MolSuite is a desktop chemist's affordable integrated suite.

Software Link: MolSuite - Molecular modeling Software

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Maestro is the unified interface for all Schrodinger software. Impressive rendering capabilities, a powerful selection of analysis tools, and an easy-to-use design combine to make Maestro a versatile modeling environment for all researchers.

Details

Schrodinger develops state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials science research. Since its founding in 1990, Schrodinger has earned a reputation for its leadership in scientific development. Schrodinger's products range from general molecular modeling programs to a complete suite of drug design software including both ligand and structure based methods.

Maestro is the linchpin of Schrodinger's computational technology. Far more than just a visualization program, Maestro also helps researchers organize and analyze data. Maestro's intuitive interface makes setting up calculations easy and straightforward. Computed results are automatically returned and incorporated into projects for further study. Maestro's vast array of visualization options makes it possible to glean insight into molecular properties as well as detailed intermolecular interactions. Maestro is a powerful and versatile molecular modeling environment, and the portal to the most advanced science in computational chemistry.

Software link: Maestro - Molecular modeling software

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MacroModel combines leading force fields, accurate effective solvation models, and advanced conformational searching methods to provide the most complete molecular modeling package suitable for a wide array of research.

Details

The energy and properties of a chemical system depend on the exact three-dimensional molecular structure. Subtle variations in functional groups can result in dramatic differences in behavior. Force field methods that represent the potential energy of a molecule as simple functions of distances and angles between atoms have proven to be an efficient and effective approach to obtaining accurate relative energies for chemical systems. The efficiency of force field-based calculations allows the exploration of large portions of the conformational space, revealing the detailed relationship between structure and energy.

Force field-based molecular modeling is routinely applied to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex.

Software Link: MacroModel - Molecular modeling software