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.
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.
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.
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.
uLan Driver provides 9-bit character message- oriented communication protocol that is transferred over an RS-485 link. The physical layer consists of one twisted pair of leads, and RS-485 transceivers. Supported hardware includes OX16C954 PCI based add-on cards, USB-to-uLan converters, the i82510 RS-485 card, or simple active converter dongle for standard PC RS-232 ports. The whole set of libraries and support tools is available for building embedded devices. They range from low level firmware boot-loaders and debugging tools up to object oriented properties browsing and manipulation and process data communication channels mapping.
Folding@home simulates protein folding. We do not entirely understand how proteins actually operate, but one important step is to study how proteins self-assemble or "fold." This is an extremely computationally intensive task since proteins take in the order of microseconds to milliseconds to fold, yet we can only routinely simulate over nanosecond to microsecond time scales. This system provides a new way to simulate protein folding that can break the millisecond barrier by dividing the work between multiple processors. Thus, with 1000 processors, we can break the millisecond barrier and help unlock the mystery of how proteins fold.
JMV (The Java Molecular Viewer) is a molecule viewer program/component written in Java and Java3D. It is designed to be an easy-to-use, platform neutral molecular visualization tool which can be used standalone or integrated into a larger program. It provides several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities. It loads PDB files over the web, from the RCSB protein databank, from BioCoRE filesystems, and from local filesystems. The interface can be customized by users, and can be disabled for web-based presentations of molecules to save browser space.
Cyberbrau is a Web-based program to help the homebrewer. It allows for very simple and intuitive beer, cider, and mead recipe creation, and it automatically calculates all the pertinent information based on the selected ingredients and schedule. In addition to the recipes, it allows multiple brewers to privately track their own batches, emailing them on racking, bottling, and lagering dates. Finally, it has a 'taster's review' section which allows those who try your brew to rate and comment on the batch. This information goes into the overall recipe ranking.