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.
News: StrBioLib 1.2 released on June 7, 2007.
Reference: If you publish research in which you used StrBioLib, please cite:
- Chandonia, JM. 2007. StrBioLib: a Java library for development of
custom computational structural biology applications. Bioinformatics,
May 30, doi: 10.1093/bioinformatics/btm269.
Downloads and more info: Please visit the project page.
Please read the Javadoc documentation.
The strbio.org 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 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.)
The strbio library is hosted by sourceforge.net.