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MOTIVATION We introduce the iRMSD, a new type of RMSD, independent from any structure superposition and suitable for evaluating sequence alignments of proteins with known structures. RESULTS We demonstrate that the iRMSD is equivalent to the standard RMSD although much simpler to compute and we also show that it is suitable for comparing sequence(More)
Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify close homologues of the sequences within the PDB database. These PDB structures are used as templates to guide the alignment of the original sequences using structure-based sequence(More)
We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify the gene sequence. This gene sequence is(More)
UNLABELLED The APDB webserver uses structural information to evaluate the alignment of sequences with known structures. It returns a score correlated to the overall alignment accuracy as well as a local evaluation. Any sequence alignment can be analyzed with APDB provided it includes at least two proteins with known structures. Sequences without a known(More)
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