Web tools and servers ...
SABLE: Relative Solvent AccessiBiLitiEs, transmembrane regions and secondary structures prediction server. In addition to making predictions for proteins of unknown structure, the SABLE server can be also used to generate graphical representations of the secondary structures and/or solvent accessibilities for known structures and for predictions obtained using other servers.
POLYVIEW: Predicted and known (using PDB codes or structures provided by the user) secondary structures and relative solvent accessibilities can be displayed using flexible 2D representations, allowing one to highlight specific, e.g. polymorphic, amino acid residues.
LOOPP: Learning Observing and Outputting Protein Patterns program and server for protein structure prediction and design of folding potentials. LOOPP has been successfully applied to a number of difficult fold recognition targets. We have also applied LOOPP to develop a number of improved folding and threading potentials (scoring functions for protein recognition). The previous version of the program was developed at Cornell, where you can find the original LOOPP server.
SIFT: Sequence Independent Filtering Tool server for ranking decoy structures from protein folding simulations, based on sequence independent measures of packing, such as the shape of mean inter-residue radial distribution function. SIFT can be used to filter out non-physically packed decoy structures from de novo or ab initio folding simulations, such as Rosetta by D. Baker and colleagues.
CinClass: The Cincinnati Classifier server provides on-line access to a number of machine learning techniques and public domain packages for supervised classification. Several new methods that we have developed are available via this interface as well. The results are represented graphically using our new "class-centric view". Still under development.
LP-ML Bench: A collection of Linear Programming and Machine Learning Benchmarks and problems, derived mostly from the applications of LP-based optimization protocols to the design of scoring functions for protein structure prediction and LP-based consensus classifiers. Still under development.
WebEditor: an on-line tool to share information with collaborator (internal use only)