226 projects tagged "Bioinformatics"
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.
Updated 02 Mar 2001
Wat2ions
| Pop | 12.92 |
|---|---|
| Vit | 1.00 |
Wat2ions is complementary to DelPhi, the renowned solver of the Poisson-Boltzmann equation. The electrostatic potential map pre-computed by DelPhi is used to replace a certain number of the water molecules of the bath, surrounding a solvated macromolecule, with ions. The potential on the oxygens of the water molecules is estimated using a 3D cubic spline interpolation of the pre-computed potential. The waters with the largest potential are replaced with chlorides, and the waters with the smallest potential, with sodii. No two ions are placed closer than a certain distance to each other. The coordinates of the macromolecule, the water bath (except the replaced waters), and the placed ions are output to a new PDB file.
Updated 26 Jun 2001
EASEA
| Pop | 49.80 |
|---|---|
| Vit | 1.42 |
EAsea Specification of Evolutionary Algorithms (EASEA), is a high-level language dedicated to the specification of evolutionary algorithms. The language and compiler are quite mature. EASEA compiles .ez specification files into C++ or Java object files, using existing evolutionary libraries. Supported C++ libraries currently are GALib or EO.
Updated 23 Aug 2005
Isotopic Pattern Calculator
| Pop | 38.21 |
|---|---|
| Vit | 3.92 |
IPC (Isotopic Pattern Calculator) is a tool for mass spectrometry that calculates the isotopic distribution of a given chemical formula or peptide sequence. It uses gnuplot to visualize the results.
