Search Results for "alpha"

This project is an interactive viewer for 3D virtual screening data.

The Diffraction Image Experiment Repository (DIMER) is an online archive for diffraction experiments, providing secure storage during analysis and publishing of experiments so they can be linked to, searched, and integrated into other databases.

This will be next version of PHIbase.

This application is intended to help students with the basics of chemistry. It can solve basic gas laws equations, and find the molar mass of a compound or element. These tasks allow students to cut the repetition out of basic chemistry.

Stochastic Pi Machine (SPiM), created by Microsoft, is a programming language for modeling biological processes. Two tools are available from Microsoft for simulation. A web application Visual SPiM, and a destkop application SPiM Player. Both simulation tools require to be run on a Windows platform. Fortunately Microsoft has also released a command line version for Linux and Mac OS based on OCAML however this version will only output a CSV file for the simulation results....

Modified version of AutoGrow, autogrow.ucsd.edu/ , with a mutation script added in the class files, and a global change of the defined mutation point from Hydrogen atoms to Calphas, to allow placement of Amino Acids. Deposited are 3 versions, used for my PhD Thesis. These allow for mutation of short 2-15 amino acid peptides, and associated screening of these using AutoDock or AutoDock Vina, allowing for 8 CPU systems to screen 10K peptides a day or 1-2K with flexible residues added in. A...

From a pdb file, the java program calculates the van der Walls surface of the protein in the file.

The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!

The Molwind project aims at developing Open Source software to visualize relationships among molecular entities such as chemical structures on the basis of NASA WorldWind. Different levels of complexity get visible by zooming in areas of interest.

Agent-based multiscale model of cancer proliferation dynamics

PepArML: An unsupervised, model-free, combining peptide identification arbiter for tandem mass spectra via machine learning.

Rosetta is a molecular language framework written in Java and based on Octet.

Ninja is an object oriented toolkit for manipulating InChI identifiers.

JPhysChem - a mathematical modeling toolbox designed to provide an abstract layer and a comprehensive graphical front-end for general model building and specific modeling and data processing in the field of mass spectrometry and physical chemistry.

A system for temperature and spectrum acquisition control in hyperfine interaction research.

FORce based Cluster Editing (FORCE) is a Java software heuristically solving the graph cluster editing problem on weighted edges using BLAST E-values. It further provides a training mode for heuristic parameter estimation.

Octet is an object-oriented molecular representation framework written in Java.

IntiMap is a convenience tool to run the MS-DOS command-line tool MapPop for selective genotyping. It adds facilities to prepare genotyping data files, manage genotype sets and visualize mapping results (genetic marker maps).

2-D chemical structure drawing program

The Octet-CDK interoperability package.

Optimal assignment-based similarity functions for chemical graphs. The approaches represent extensions of the Optimal Assignment Kernel of Fröhlich et al.

Crude Metabolic Pathway Analysis visualization software. For a software engineering class.

A simple tool for molecular biologists (or similar) to estimate the size of electrophoresis gel bands. This can be applied to SDS-Page-,Native-Protein-, DNA, RNA, *whatever* gels as long as a weight/size standard lane is present on the gel.

PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management.Statistical validation, , visualization, and converters from raw MS data open mzXML mzData format