Bonnie Berger

  Public-Domain Computing Resources
The PairCoil2 program predicts coiled-coil domains in protein sequences by using pairwise residue correlations obtained from a coiled-coil database. The original PairCoil program is still available for use.
The MultiCoil program predicts the location of coiled-coil regions in amino acid sequences and classifies the predictions as dimeric or trimeric. An updated version, Multicoil2, will soon be available.
LearnCoil Histidine Kinase
The LearnCoil Histidine Kinase program uses an iterative learning algorithm to detect possible coiled-coil domains in histidine kinase receptors.
LearnCoil VMF
The LearnCoil-VMF program uses an iterative learning algorithm to detect coiled-coil-like regions in viral membrane-fusion proteins.
  Structure Discovery Tools
  The Trilogy program discovers novel sequence-structure patterns in proteins by exhaustively searching through three-residue motifs using both sequence and structure information.
  The ChainTweak program efficiently samples from the neighbourhood of a given base conformation by iteratively modifying a conformation using a dihedral angle representation.
  The TreePack program uses a tree-decomposition based algorithm to solve the side-chain packing problem efficiently. This algorithm is more efficient than SCWRL 3.0 while maintaining the same level accuracy.
  Beta-Structure Prediction
  The BetaWrap program detects the right-handed parallel ß-helix super-secondary structural motif in primary amino acid sequences by using ß-strand interactions learned from non-ß-helix structures.  
  Wrap-and-Pack detects ß-trefoils in protein sequences by using both pairwise ß-strand interactions and 3-D energetic packing information.
  The BetaWrap Pro program predicts right-handed ß-helices and ß-trefoils by using both sequence profiles and pairwise ß-strand interactions, and returns coordinates for the structure
  Comparative Genomics
  GLASS aligns large orthologous genomic regions using an iterative global alignment system. Rosetta identifies genes based on conservation of exonic features in sequences aligned by GLASS.
  The MSARi program identifies conserved RNA secondary structure in non-coding RNA genes and mRNAs by searching multiple sequence alignments of a large set of candidate orthologs for correlated arrangements of reverse-complementary regions.
  Systems Biology
  t-sample is an online algorithm for time-series experiments that allows an experimenter to determine which biological samples should be hybridized to arrays to recover expression profiles within a given error bound.

The Struct2Net program predicts protein-protein interactions (PPI) by integrating structure-based information with other functional annotations, e.g. GO, co-expression and co-localization etc. The structure-based protein interaction prediction is conducted using a protein threading server RAPTOR plus logistic regression.


IsoRank is an algorithm for global alignment of multiple protein-protein inter- action (PPI) networks. The intuition behind our algorithm is that a protein in one PPI net- work is a good match for a protein in another network if the former's neighbors are good matches for the latter's neighbors.