Burkhard Rost: Catalogue of software

The following programs have been developed and written by B Rost. Most methods have been published in journals.

List of programs

• (1) PHDsec Neural network system for the prediction of protein secondary structure from multiple sequence alignments (Profile-based neural network system from HeiDelberg).
• (2) PHDacc Neural network system for the prediction of residue solvent accessibility from multiple sequence alignments.
• (3) PHDhtm Neural network system for the prediction of the location of transmembrane helices in integral membrane proteins from multiple sequence alignments.
• (4) PHDtopology Dynamic programming-based refinement of neural network prediction of transmembrane helix locations (PHDhtm) and prediction of topology for integral membrane proteins.
• (5) PROTRON Neural network for training and testing PHDsec, PHDacc, and PHDhtm.
• (6) TOPITS/PHDthreader Program for threading one-dimensional predictions into three-dimensional structures. Combining PHD predictions with sequence alignments to detect remote homologues (<25% pairwise sequence identity).
• (7) EVALSEC Evaluation of secondary structure prediction accuracy.
• (8) EVALACC Evaluation of solvent accessibility prediction accuracy.
• (9) AQUA Assessing the quality of alignments.
• (10) PredictProtein Prediction service enabling the access of PHDsec, PHDacc, PHDhtm, PHDtopology, TOPITS/PHDthreader, EVALSEC, and MaxHom via the internet (email and WWW interface).

Availability

Executables are available for use inside EMBL. Currently, some programs may be to some extent portable. An exception is PredictProtein which is not portable at all, but it is available world-wide. Most programs will need to be updated in a timely manner. This poses a technical problem since the program essential for the updating (PROTRON) cannot currently be executed by anybody (not even by the author). Updates will require some months of programming time by the author or a scientist equivalently experienced with neural network algorithms. Making some of the essential programs portable will supposedly require between one and three months (note: time estimates according to the optimism of a scientist, i.e., in reality to be multiplied by some factor).

Interests of others

Reinhard Schneider (EMBL, Heidelberg) modified his alignment program MaxHom such that the dynamic-programming step for the threading method (6) can be accomplished. Thus, the threading program currently requires the availability of MaxHom. MaxHom is also used for the PredictProtein service. Furthermore, Reinhard Schneider helped initially in getting the PredictProtein service started.

Antoine de Daruvar (Bordeaux Univ, France) contributed a large number of scripts managing the jobs performed by PredictProtein. Antoine de Daruvar has also supervised the non-scientific part of the PredictProtein service for about a year.