In my group we develop (and release in full) software packages in the main directions of our research

moil is a general molecular dynamics package that makes it possible to perform a variety of calculations such as energy calculations, minimization, dynamics, free energy calculations and more. It has databases supporting proteins, water and DNA. Unique features of MOIL includes algorithm for the computations of reaction coordinates and long time dynamics, the Locally Enhanced Sampling algorithm, and a fully operational version (including graphic interface and a parallel version) for Windows. Non graphic versions are available for many other operating systems. Credit for moil developers can be found here.

loopp stands for Learning Observing and Outputting Protein Patterns. It is a program to annotate proteins (from sequence) as well as to learn new annotation schemes and folding potentials from data of true and false positives. The first version was written by Jaroslaw Meller with emphasis on the design of folding and threading potentials, which remains our main research focus. The second version was written by Tamar Galor-Naeh in which we also address general questions about optimization of an alignment. Jaroslaw Pillardy added the "loopp driver" that provides a general web and parallel interface and also combines results from loopp with other annotation schemes (e.g. BLAST and algorithms to predict secondary structure). Complete credit for loopp developed is here.