ArticleDatabase : the journal of biological databases and curation2025
PASS2: update of database of structure-based sequence alignments.
Article in Database : the journal of biological databases and curation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Protein sequence alignments are evolutionary models and offer as starting points for the recognition of additional members of a homologous family and design of experiments. However, the accuracy of sequence alignments is obscured at the superfamily level due to distant relationships. Where structures of proteins are available, distantly related proteins can be aligned, guided by structural features. The Protein Alignment Organized as Structural Superfamilies (PASS2) database offers such structure-based sequence alignments for protein domains classified within superfamilies, as per the Structural Classification of Proteins extended (SCOPe) framework. The present update of PASS2 (PASS2.8) corresponds to the latest SCOPe release (version 2.08). This release comprises data for 26 690 protein domains exhibiting less than 40% sequence identity, organized into 2058 superfamilies. Several features derived from these alignments, including conserved secondary structural motifs, hidden Markov models (HMMs), conserved residues, and interactions across superfamilies, are also provided. For superfamilies containing divergent members, a k-means clustering algorithm has been employed to identify outliers and partition domains into split superfamilies. Novel features in this update include topological diagrams of the domains, potential interactors for each domain, and an updated methodology for identifying conserved interactions across superfamilies. This version of the database can be reached from http://caps.ncbs.res.in/pass2.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.