149 projects tagged "Medical Science"
Updated 11 Mar 2009
ploticus
| Pop | 292.48 |
|---|---|
| Vit | 8.05 |
PLOTICUS is a command line utility for creating bar, line, pie, boxplot, scatterplot, sweep, heatmap, vector, timeline, Venn diagrams, and other types of charts and plots. ploticus is good for automated or just-in-time graph generation. It handles date, time, and categorical data nicely, and has some basic statistical capabilities. It can output to GIF, PNG, SVG, SWF, JPEG, PostScript, EPS, and X11. You can use convenient preset options or create complex scripts with rich and detailed color and style operations.
Updated 14 Feb 2012
VMD
| Pop | 132.95 |
|---|---|
| Vit | 17.13 |
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.
Updated 29 Dec 2001
The VP7 WKP
| Pop | 25.81 |
|---|---|
| Vit | 3.20 |
The VP7 Way Kool Project is a GTK application which simulates a laboratory experiment with radioactive nuclei. The user can choose between many predefined radioactive sources or create new ones. The number of decayed nuclei and the activity of the source can be determined with a built-in counter. The beam can be attenuated with shields of paper, aluminium, and/or lead.
Updated 16 Mar 2006
CatDCD
| Pop | 23.07 |
|---|---|
| Vit | 1.85 |
CatDCD functions much like the Unix "cat" command: it concatenates DCD files into a single DCD file. You can also use CatDCD to write only selected atoms to the final DCD file.
Updated 02 Mar 2001
FlipDCD
| Pop | 18.60 |
|---|---|
| Vit | 1.00 |
FlipDCD is a small utility for reversing the endianism of binary DCD trajectory files from Charmm and NAMD. This can be useful when running simulations on one architecture and visualizing or analyzing the results on another. FixDCD is a tiny utility to modify the header of an X-PLOR DCD file to make it readable by programs expecting Charmm DCD files, at the expense of a Timestep size value in the header.
Updated 02 Mar 2001
MatDCD
| Pop | 18.06 |
|---|---|
| Vit | 1.00 |
MatDCD is a Matlab package for reading/writing DCD-formatted molecular dynamics trajectory files. It supports Charmm and xplor-format DCD files, it can read both big- and little-endian storage formats, and it can specify which atom indices to load without having to load the entire file.
Updated 02 Mar 2001
Mindy
| Pop | 18.49 |
|---|---|
| Vit | 1.00 |
Mindy is a very simple serial molecular dynamics program derived from NAMD source code. It currently uses xplor parameter and structure files. The program is written in very straightforward C++.
Updated 02 Mar 2001
Mol_Volume
| Pop | 17.20 |
|---|---|
| Vit | 1.00 |
Mol_Volume calculates the volume of a macromolecule by a method somewhat akin to the Monte Carlo method, namely, by measuring how many vertices of a dense regular grid happen to be within the probe radius of the molecule's atoms. The volume is then calculated as V = V_grid * N_near / N_total = N_near * V_per_node.
Updated 02 Mar 2001
PDBCat
| Pop | 18.92 |
|---|---|
| Vit | 1.00 |
PDBCat can be used to manipulate and process PDB files using commonly available text-processing tools such as Perl, awk, etc. The Brookhaven Protein Data Bank stores atomic coordinate information for protein structures in a column-based format which is designed to be read easily read by FORTRAN programs. PDBCat converts the ATOM and HETATM records of PDB files from this column-based format to a field-based one that is more easily processed by standard Unix tools.
Updated 02 Mar 2001
SODIUM
| Pop | 17.83 |
|---|---|
| Vit | 1.00 |
SODIUM places the required number of sodium ions around a (simulated) system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex). The ions are placed in the nodes of a cubic grid in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy. The coordinates of the placed ions are printed out in the PDB format for further usage. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.
