TERMs – tertiary motif (TERM)-based structure mining.
MASTER – a fast RMSD-based structure search tool (Method of Accelerated Search for Tertiary Ensemble Representatives).
MaDCaT – a distance map-based protein structure search tool (Mapping of Distances for the Categorization of Topology).
DrawCoil 1.0 – a web-based program for creating coiled-coil helical wheel diagrams.
CCCP – Coiled-Coil Crick Parameterization; programs for fitting Crick parameters to coiled-coil structures and generations of ideal structures from parameters.
CLEVER 1.0 – Cluster Expansion Version 1.0; a C++ package for the application of the Cluster Expansion (CE) methodology. CE can be used to express any protein property as an analytical function of the amino-acid sequence.
MSL – an open source C++ library for analysis, manipulation, modeling and design of macromolecules.
ConFind – a tool for identifying mutually influencing pairs of positions in proteins.
TERM-ddG – a TERM-based method for computing stability changes in proteins upon mutations.
Dynamics Derivatives – a mathematical treatment of Cartesian gradients of internal degrees of freedom (distance, angle, dihedral angle).