RSS 82 projects tagged "Medical Science"

Download Website Updated 22 Sep 2006 JChemPaint

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Pop 172.49
Vit 9.11

JChemPaint is a program for drawing 2D chemical structures like those found in most chemistry textbooks.

No download Website Updated 16 Mar 2006 CatDCD

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Pop 20.64
Vit 1.80

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.

Download Website Updated 02 Mar 2001 FlipDCD

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Pop 16.25
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.

Download Website Updated 02 Mar 2001 MatDCD

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Pop 17.15
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.

Download Website Updated 02 Mar 2001 Mindy

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Pop 17.26
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++.

Download Website Updated 02 Mar 2001 Mol_Volume

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Pop 16.06
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.

Download Website Updated 02 Mar 2001 PDBCat

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Pop 18.28
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.

Download Website Updated 02 Mar 2001 SODIUM

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Pop 16.73
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.

Download Website Updated 15 Oct 2001 xsbrowser

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Pop 37.63
Vit 2.27

The xsbrowser creates a human-readable documentation of XML document types represented as XML 1.0 DTDs or XML schemas (REC-xmlschema-20010502). The user needn't understand the DTD or XML Schema syntax. The xsbrowser exploits XML Schema. Although you can directly feed a DTD into the xsbrowser, it is recommended to first translate the DTD using the dtd2xs translator. The dtd2xs translator allows a more sophisticated mapping of DTDs onto XML schemas. The only requirement is a Web browser that supports Java applets, Javascript, and CSS1. The Web browser needn't support XML.

Download No website Updated 08 Jul 2001 GNotary Digital Notary Service

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Pop 32.51
Vit 1.00

GNotary is a set of Python scripts that implement an asynchronous digital notary service. Anybody who needs certification of any digital document creates a message digest (like MD5 or RIPEMD160) of that document and submits it to the GNotary service by email. GNotary signs this email digitally (using GnuPG), retains a copy of the certified and time stamped message, and mails it back to the sender, optionally with the public key attached to allow the sender to verify the signed document. At regular intervals, the GNotary server creates message digests of its own logs and distributes them among other GNotary servers, thus making it virtually impossible to forge the chain of evidence that authenticates a submitted document.

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ToPIA

A persistence and application distribution framework.

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Collax Business Server

An all-in-one Linux server for small- and medium-sized businesses.