gmx_makecyclictop -- A Perl script to create a cyclic peptide or cyclic nucleotide topology file for GROMACS molecular dynamics simulations.
dali_sp -- A wrapper script for Dali to perform serial structure comparison and to merge output pairwise alignments into single multiple alignment. After downloading the archive uncompress it with the command: tar -zxf dali_sp.tgz
modplus -- A wrapper script for Modeller; it performs sequence-structure alignment and preprocessing steps to model target sequence. The input to the program is a multiple alignment of target and template sequences in the FASTA format. The template structures will be supposed to be accessible in a given location. Once downloaded, uncompress the archive with the command: tar -zxf modplus.tgz