Provides high quality reference alignments based on 3D structural superpositions. BAliBASE is a large scale benchmarks specifically designed for multiple sequence alignment. The alignment test cases are manually refined to ensure the correct alignment of conserved residues. The alignments are organized into reference sets designed to represent real multiple alignment problems.
Tests multiple sequence alignment methods. PREFAB is a test set which exploits methodology, test data and statistical methods that have previously been applied to alignment accuracy assessment. It contains (i) a set of reference pair alignments, (ii) samples of sequences for testing multiple alignment programs and (iii) a program of assessing the quality of work of multiple alignment programs.
Gathers comparison of protein structures. DBAli is a database that contains pairwise and multiple structure alignments of protein structures in the Protein Data Bank (PDB). It also includes five tools that use the structural relationships in the repository. These tools can be employed to annotate the functions of protein structures whose functions are not yet known. The database also provides links to the MODBASE, LigBase, PIBASE, PDB, CATH, SCOP, PFamA, InterPro, Enzyme and GO databases.
Provides access to data from studies on direct coupling analysis (DCA) ability to differentiate between properly folded and misfolded structures. DCA vs. Misfolds is dedicated to studies on DCA, a method that can assist researchers in studying protein structure.
Provides access to multiple structure alignments for all protein families in the Protein Data Bank (PDB). DMAPS is a database of multiple alignments for protein structures containing data classified by several functional and structural criteria. The alignments are available in a variety of formats for further use. The database can be useful for an array of research projects in structural bioinformatics, such as building structure-based family profiles and patterns, improving the quality of sequence alignments and finding remote homologues.
Provides a data resource of structural alignments. SAD chooses a good alignment from several candidates via an alignment quality measure. This database uses alignments from multiple other databases and an ab initio method named internal coordinate mechanics (ICM) global structural alignment. It uses also the contact alignment quality score, a scoring function, to assess trial alignments by their statistical significance associated with their ability to reproduce conserved three-dimensional residue contacts.