strbio.org is run by
John-Marc Chandonia, firstname.lastname@example.org.
The StrBio library is a set of Java classes useful for development of
software for computational structural biology research. They are
licenced under the LGPL.
These classes are the basis for several published research projects,
including the Pred2ary secondary structure prediction program and the
ASTRAL database of protein domain sequences.
The library is hosted at sourceforge.net. For
downloads and other information, please visit the project page.
documentation is also available.
The most interesting structural biology applications included are:
- Pred2ary protein secondary structure prediction
- JThread protein fold prediction
- ConvertProtein for interconversion of protein file formats (FASTA, PDB, MSF, ALN, CASP, DSSP, HSSP, YAPF)
- Filters to exchange data with commonly used molecular biology applications (e.g., BLAST, MinArea, MODELLER)
- MakeRAF tool to create the Rapid Access Format sequence maps for the ASTRAL database.
Other more general-purpose functionality that is included:
- Neural network library, including Scaled Conjugate Gradient or Steepest Descent optimization
- Hooke and Jeeves derivative-free global optimization algorithm
- Misc mathematical objects and algorithms (vectors, matrices, etc)
- Efficient string formatting using Printf-based syntax (printf, atoi, atof, etc.)