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Updated: May 6, 2026

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Published on: October 3, 2018
LenVarDB: database of length-variant protein domains
Eshita Mutt1, Oommen K Mathew, Ramanathan Sowdhamini
1International Institute of Information Technology-Hyderabad, Gachibowli, Hyderabad 500032, Andhra Pradesh, India, National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India and SASTRA University, Tirumalaisamudram, Thanjavur 613401, Tamil Nadu, India.
LenVarDB traces protein domain length variations (indels) across millions of sequences and protein families. Visualizing these evolutionary changes aids in predicting functional impacts and designing bioengineering experiments.
Area of Science:
- * Molecular Biology
- * Bioinformatics
- * Evolutionary Biology
Background:
- * Protein domains are key functional and structural units driving protein diversity.
- * Evolutionary mechanisms like amino acid substitutions and indels (insertions/deletions) modify protein domains.
- * Length variations (indels) significantly impact protein structure, function, and interactions.
Purpose of the Study:
- * To develop LenVarDB, a database for tracing length variations in protein domains.
- * To analyze indels across 731 protein superfamilies and over 2.7 million sequences.
- * To provide visualization tools for understanding indel location and potential functional consequences.
Main Methods:
- * Utilized structure-based sequence alignments from the PASS2 database.
- * Mapped identified length variations onto protein structures and sequence alignments.
- * Analyzed indel proximity to active sites to infer functional impact.
Main Results:
- * Cataloged length variations across 731 SCOP-based protein domain superfamilies.
- * Identified and visualized indels in relation to protein structure and sequence alignments.
- * Demonstrated the utility of indel location data for predicting functional site alterations.
Conclusions:
- * LenVarDB offers a valuable resource for studying evolutionary changes in protein domains.
- * Visualizing indel positions aids in understanding their role in protein function and evolution.
- * The database supports bioengineering efforts by highlighting potentially impactful length variations.
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