CopraRNA (Comparative Prediction Algorithm for sRNA Targets) is a tool for sRNA target prediction. It computes whole genome predictions by combination of distinct whole genome IntaRNA predictions. As input, CopraRNA requires at least 3 homologous sRNA sequences from 3 distinct organisms in FASTA format.
Jali (Jumping Alignments) is an alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Watherman algorithm.
MolIDE is an open-source cross-platform graphical environment for homology modeling. It implements the most frequently used steps involved in modeling: sequence search, secondary structure prediction, multiple-round psiblast alignments, assisted alignment editing (integrating a template viewer and secondary structure prediction), side chain replacement and loop building. MolIDE takes an input target sequence and uses PSIBLAST to identify and align templates for comparative modeling of the target. The sequence alignment to any template can be manually modified within a graphical window of the target–template alignment and visualization of the alignment on the template structure. MolIDE builds the model of the target structure on the basis of the template backbone, predicted side.
HOMA (Homology Modeling Automatically) is a web-based interface that can create homology models of a protein with unknown structure (the target or query protein) based on a homologous protein with known structure (the template protein).
iMembrane is a homology-based method, which predicts a membrane protein’s position within a lipid bilayer. It projects the results of coarse-grained molecular dynamics simulations onto any membrane protein structure or sequence provided by the user.