Molecular Simmulation
Molsketch is a 2D molecular editing tool. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 270.32 KB | Download (44): Molsketch Download |
Given the chemical formula, MolWgt calculates the molecular weight of a substance.
Platforms: Mac, BSD, Linux
License: Freeware | Size: 2.47 KB | Download (44): MolWgt Download |
NOC is a open source development toolkit and a powerful molecular explorer for protein structure visualizing,analysis,crystallographic mapping, modeling, and refinement, Gromacs/Amber MD trajectories displaying,movie making...
Platforms: Windows, Mac, BSD, Linux
License: Freeware | Size: 5.75 MB | Download (49): NOCH Download |
A database to handle voucher specimens of DNA sequences used for molecular phylogenetics.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 1.23 MB | Download (53): NSG's voucher specimen database Download |
Octet is an object-oriented molecular representation framework written in Java.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 284.03 KB | Download (44): Octet Download |
'Plasmidb' is a database management system (RDMS) used to manipulate, view and store molecular biology information rapidly and easily. Editable information includes: constructed plasmids, clones, standard vectors, primers, antibiotics, enzymes and more
Platforms: Windows, Mac, Linux
License: Freeware | Size: 53.34 MB | Download (45): Plasmidb Download |
PSI is an open-source program for computing molecular properties using high-accuracy, ab initio, quantum mechanical models.
Platforms: Mac, BSD, Linux
License: Freeware | Size: 7.07 MB | Download (45): psicode Download |
A 3D viewer for molecular charge distributions.Implemented in OpenGL with GLUT.Includes a small OpenGL windowing library/widget set.
Platforms: Windows, Mac, BSD, Linux
License: Freeware | Size: 329.95 KB | Download (48): VASP Data Viewer Download |
A utility for animating molecular vibrations. Normal modes are read from a file automatically determined to be from Aces2, Gamess, PC Gamess, Gaussian 90/92/95/94/98, ADF, Dalton, Jaguar, MOPAC, or Spartan.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 36.22 KB | Download (46): xvibs Download |
The Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and...
Platforms: Windows, Mac, *nix, Python, BSD Solaris
License: Freeware | Download (58): The Python Macromolecular Library Download |
Matlab procedure that generates a Surface Plasmon Resonance profile to compare it with experimental data. Relevant parameters are given as graphical input.A 90dlT- prism is assumed, the reflected intensity is plotted against the external angle. It can be plotted on its own, or compared to a file...
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (45): Surface Plasmon Resonance Calculator Download |
HOT is a package originally constructed for combustion modeling in Matlab. It calculates common thermodynamic properties such as enthalpy, specific heat, entropy, internal energy, gamma, ideal gas constant, molecular weight, etc
Platforms: Matlab
License: Freeware | Size: 143.36 KB | Download (40): HOT Thermodynamic Tools for Matlab Download |
MolMass is a function for calculating the molar weight of a substance given in form of a chemical formula.Function call: MM = MolMass(substance)Substance is a string of the chemical formula of a substance.Example: MM = MolMass('Fe2(SO4)3');Substance can also be a vector of substances opened by...
Platforms: Matlab
License: Freeware | Size: 102.4 KB | Download (46): Molecular Weight Calculator Function Download |
The Mole Package contains 3 mfiles and 1 matfile. molecules2 calculates molecular masses pertable provides data on the elements sym2an converts a chemical symbol to a valid atomic number (useful for molecules2 and pertable). atoms contains atomic number data.
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (49): Mole Package Download |
Seqlib is a Python module and application package for population genetics (and more). It allows processing, analyzing and simulating biological sequences. It is specifically designed for automated large-scale sequence analysis. Main features: * Fasta-centered input and output, format...
Platforms: Mac
License: Freeware | Size: 2.7 MB | Download (37): SEQLIB Download |
MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively...
Platforms: Mac
License: Freeware | Size: 19.01 MB | Download (42): MDAnalysis Download |
How do you know if a chemical equation is balanced? What can you change to balance an equation? Play a game to test your ideas! Sample Learning Goals * Balance a chemical equation. * Recognize that atoms are conserved in a chemical reaction. * Describe the difference between coefficients and...
Platforms: Mac
License: Freeware | Size: 1.37 MB | Download (35): Balancing Chemical Equations Download |
Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Toxtree could be applied to datasets from various compatible file types. User-defined molecular structures are also supported - they could...
Platforms: Mac
License: Freeware | Size: 55.79 MB | Download (36): Toxtree Download |
The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. The package's current capabilities include a variety of Hartree-Fock, coupled cluster, complete-active-space self-consistent-field, and...
Platforms: Mac
License: Freeware | Size: 7.07 MB | Download (36): PSI3 Download |
analyzes different features of multiple primers simultaneously, the melting temperature calculation for standard and degenerate oligonucleotides, GC content, primer PCR efficiency; primers are analyzed for all primer secondary structures including G-quadruplexes detection, hairpins, self-dimers...
Platforms: Mac
License: Freeware | Size: 10.24 KB | Download (43): PrimersList Download |