MOTIVATION: Similarities in core residue packing provide evidence for divergence or convergence not reported using other methods. RESULTS: We apply a new method for rapid structure comparison based on Simplicial Neighborhood Analysis of Protein Packing (SNAPP) to the diverse structural classification of proteins (SCOP) alpha/beta-class of protein folds. The procedure identifies inter-residue packing motifs shared by protein pairs from different folds. A threshold of 0.67 A RMSD for all atoms of corresponding residues ensures inclusion of only highly significant similarities comparable with those observed for identical catalytic residues in homologues. Many tertiary packing motifs are shared among the three classical Rossmannoid folds, as well as thousands of other motifs that occur in at least two distinct folds. Merging of neighboring packing motifs facilitated recognition of larger, recurrent substructures or cores. The anti-codon-binding domain of an archeal aminoacyl-tRNA synthetase (aaRS) was discovered to possess a packed core in which eight identical amino acid residues are within 0.55 A RMSD of the comparable structure in the FixJ receiver, a member of the Rossmannoid family that also includes the CheY signaling protein and flavodoxin-like proteins. Further investigation identified close variants of this core in five other Rossmannoid folds, including a functionally relevant core in Class Ia aminoacyl-tRNA synthetases. Although it is possible that the two essentially identical cores in the ProRS anti-codon-binding domain and the FixJ receiver converged to the same structure, the consensus core obtained from the structural and sequence alignments suggests that all the implicated protein folds descended from a simpler ancestral protein in which this core provided nucleotide binding and proto-allosteric functions. AVAILABILITY: Programs are available at http://staff.vbi.vt.edu/cammer/snapp/download/ IMPLEMENTATION: Programs were written in Perl and c and run under Linux. CONTACT: [email protected].

UNLABELLED: SChiSM2 is a web server-based program for creating web pages that include interactive molecular graphics using the freely-available applet, Jmol, for illustration. The program works with Internet Explorer and Firefox on Windows, Safari and Firefox on Mac OSX and Firefox on Linux. AVAILABILITY: The program can be accessed at the following address: http://ci.vbi.vt.edu/cammer/schism2.html.

Abstract Summary: SChiSM is a program for creating World Wide Web (WWW) pages that include embedded interactive molecular models using the browser plug-in, Chime, for visualization. The program works with Netscape 4.x and Internet Explorer 5 browsers to facilitate Chime/Rasmol scripting control of a molecular display. Availability: The program can be accessed from the following address: http://mmlsun2.pha.unc.edu/schism.html. Contact: [email protected]