Protein Sequence Analysis and Modelling

pSAAM FOR WINDOWS©

INTRODUCTION
The program pSAAM for Windows© is derived from the program AMPHI, which is a component of the SEQANAL package written by A.R. Crofts to assist in analysis of protein sequences for information about secondary and tertiary structure(15). This new program expands considerably the options available for Protein Sequence Analysis and Modelling, and provides a more user-friendly environment. The program is menu driven and mouse activated. Most functions are fairly intuitive, and a series of on screen Help menus allows most options to be used easily without reference to the manual. This document contains all the information in the Help menus, and expanded information on installation, file format, and support packages. PSAAM contains all the functions found in AMPHI, and will replace AMPHI in future versions of the SEQANAL package. Several new features have been added.

- a Ribosome function allows the user to generate atomic coordinates for models and to file them in the format of the Brookhaven Protein Data Bank (.PDB format) (16, 17). The 3-D models can then be viewed and manipulated using any Molecular Graphics package which reads files in this format, such as the program pdViewer for Windows.

- a Seq Plot option allows the user to compose on the screen a 2-D structural model based on analysis of the sequence, using helical cylinders, helical wheels and coils. The composition phase is interactive, and the user choses size, orientation, position and rotation of the helices, and the position of each residue in coils. The composed picture can then be plotted as a model on the Windows printer. Helices produced in the Seq Plot window can be used to construct stand-alone Models of proteins.

-a Prediction Aids window runs Eisenberg diagrams, Finer-Moore diagrams, and Prediction Profiles. The prediction profiles use a new set of secondary structure probability data generated by Laura Walsh and A.R. Crofts by analysis of the protein structural data base for structural environment as well as for secondary structural type.

The program brings to the Windows© environment a self contained package for analysis of protein sequence data. Companion programs in the pSAAM package are INFORMAT and FINDSEQ. The programs have been written to allow compatability with the file formats used by the ENTREZ interface with GenBank, and the MACAW program for sequence alignment, both provided by NCBI (National Center for Biotechnology Information). Together with pdViewer for Windows©, the program also provides a convenient tool for examination of protein structure and physical chemistry, and for structural prediction, and an environment for building two or three dimensional models of structures derived from analysis of sequence data, prediction, and comparison with known structures.