Category:Portfolio

Web servers

Below are a list of web servers and/or web services I have worked on or am currently working on.

• TLS Motion Determination (TLSMD) / Python Macromolecular Library (mmLib): analyzes a protein crystal structure for evidence of flexibility.

Server administrator and developer; October 2006–October 2010.

The Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, and PDB files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer. The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization. This includes specialized classes for proteins, DNA, amino acids, and nucleic acids. Also included is a extensive monomer library, element library, and specialized classes for performing unit cell calculations combined with a full space group library.

• Raster3D: a set of tools for generating high quality raster images of proteins or other molecules.

Starting with version 2.7s, created a port to Mac OS X as well as compile binaries using the Intel Fortran Compiler. Also added png/jpeg (and labels) output using libgd. Added a new feature in rastep to support Skittles validation (introduced in 2.9); February 2009–July 2010.

• FastContact Server: a free energy scoring tool for protein-protein complex structures.

Version 2.0: Programmer, Server architect, and administrator; January 2007–June 2007.

Version 1.0: Programmer, Server architect, and administrator; July 2005–December 2006.

• SmoothDock Server (under development): a fully automated algorithm for finding physical interactions between proteins.

Programmer, Server architect, and administrator; January 2005–present (note: This server uses code optimised and run in parallel on 256 processors).

• CBS Fungal Database: DNA structural atlases for complete chromosomes and genomes.

Programmer, Server architect, and administrator; August 2005–December 2005.

• LooseLoops Server (under development and construction): predicts regions of a protein (PDB format) having highly flexible loops

Programmer, Server architect, and administrator; November 2004–June 2006.

• DomainSplit Server: predicts the number of domains in a given protein (PDB format)

Server architect and administrator; September 2004–June 2006.

• ZHunt Online Server: predicts the locations of probable Z-DNA forming regions in a given DNA sequence

Primary researcher and programmer; May 2000–September 2004 (note: front end by Sandor Maurice; back end by Sandor Maurice and P. Christoph Champ)

• Able2Know.com:

An administrator and developer; January 2005–present.

See also

• Curriculum Vitae