PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies

Abstract

PASS2 is a nearly automated version of CAMPASS and contains sequence alignments of proteins grouped at the level of superfamilies. This database has been created to fall in correspondence with SCOP database (1.53 release) and currently consists of 110 multi-member superfamilies and 613 superfamilies corresponding to single members. In multi-member superfamilies, protein chains with no more than 25% sequence identity have been considered for the alignment and hence the database aims to address sequence alignments which represent 26 219 protein domains under the SCOP 1.53 release. Structure-based sequence alignments have been obtained by COMPARER and the initial equivalences are provided automatically from a MALIGN alignment and subsequently augmented using STAMP4.0. The final sequence alignments have been annotated for the structural features using JOY4.0. Several interesting links are provided to other related databases and genome sequence relatives. Availability of reliable sequence alignments of distantly related proteins, despite poor sequence identity and single-member superfamilies, permit better sampling of structures in libraries for fold recognition of new sequences and for the understanding of protein structure-function relationships of individual superfamilies. The database can be queried by keywords and also by sequence search, interfaced by PSI-BLAST methods. Structure-annotated sequence alignments and several structural accessory files can be retrieved for all the superfamilies including the user-input sequence. The database can be accessed from http://www.ncbs.res.in/%7Efaculty/mini/campass/pass.html.

PASS2: an automated database of protein alignments organised as structural superfamilies

“…Diversification of structural members may be studied in terms of the dissimilarity of structure or divergence of the sequences. The database has been linked to other useful protein databases as in the previous version of PASS2 [15]. …”

“…Analyses of structural and sequence differences amongst known superfamily members can hopefully provide useful guidelines for modelling distantly related proteins. PASS2 database [14,15] presents alignments of sequentially distant proteins related at the superfamily level. We report an automated, updated version of the superfamily alignment database that is in direct correspondence with SCOP (1.63) database.…”

Regions of minimal structural variation among members of protein domain superfamilies: application to remote homology detection and modelling using distant relationships

“…Further, this method is not iterative in nature. But, the average specificity for all the 110 superfamilies in PASS2 database [11] is 86% and the average sensitivity is around 70% (Fig. 5(a)).…”

“…Deviation of the average distances of the templates with respect to the centre of mass of the protein (b) also shows similar distribution. recorded in PASS2 [11] database, have been scanned in a database of protein entries from the structural databank [12,13] using SCANMOT algorithm. This multi-motif procedure does not employ the query sequence except to note the inter-motif spacing.…”

Computational Biology and Bioinformatics: A tinge of Indian spice

“…The current generation of Indian computational biologists effectively exploited these pivotal points and drifted steadily towards global trends such as integration of biological data, development of useful suites of software and databases in biology, generation of new hypotheses on form, functions and models of evolution of biomolecules especially using genome­ wide analyses [29– 30–31 –32–33 –34– 35–36–37–38–39–40], neuronal simulations and systems biology.…”