Dnastar, Inc.

John L Schroeder

Frederick R Blattner

Michael R Slater

Steven J Darnell

Amanda E Mitchell

Michael Waterman

Matthew R Larson

Donna L Daniels

The present invention is an accelerated conformational sampling method for predicting target peptide and protein structures comprising a process of determining energy minimized synthetic templates using a simple system for modeling individual molecular bonds within the subject peptide or protein. Use of these synthetic templates greatly reduces the computational resources necessary for optimally determining structural features of the target peptide or protein. The present invention also provides methods for rapid and efficient analysis of the effect of mutations on target peptides and proteins.

Protein structure prediction system

A display system for use on a digital computer is specifically designed to display information about nucleotide sequences, such as DNA sequences and the protein or amino acid sequences associated with those nucleotide sequences. The system uses a specially adapted font which includes special three letter characters representing the amino acids. The letters in the special characters are kerned for compact presentation. The use of such three letter characters, created to be of a width three times that of the remaining monospace characters in the font, allows amino acid sequences to be stored and presented with the corresponding nucleotide sequences in such a fashion that they are properly aligned and also usually legible.

Computer representation of nucleotide and protein sequences

A system and method for the construction of one-dimensional maps from fragmentation data is disclosed. Particularly useful for construction of restriction maps of DNA, the system and method completely permutes sites, single digest fragments, and any available multiple digest fragments, and displays maps in rank-order according to a quality factor. Display of constructed maps includes information about relative ordering of all fragments, sites, and particularly about closely-spaced sites and fragments.

System and method for fragmentation mapping

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Madison, WI, United States of America

John L Schroeder