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Related Experiment Video

Updated: Feb 21, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Protein Structure Modeling with MODELLER.

Benjamin Webb¹, Andrej Sali²

¹Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, CA, 94143, USA.

Methods in Molecular Biology (Clifton, N.J.)

|October 8, 2017

Summary

This summary is machine-generated.

Computational protein structure modeling bridges the sequence-structure gap. MODELLER software can generate useful protein models, achieving accurate results for over half of known protein sequences.

Keywords:

Comparative modeling Fold assignment Model assessment Multiple templates Sequence-structure alignment

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Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Genome sequencing rapidly expands known protein sequences.
Experimental protein structure determination is resource-intensive, leaving most sequences uncharacterized.
A significant gap exists between the number of known protein sequences and their experimentally determined structures.

Purpose of the Study:

To demonstrate the utility of computational protein structure modeling.
To illustrate the application of MODELLER for comparative protein modeling.
To assess the accuracy and applicability of automated modeling protocols.

Main Methods:

Utilizing MODELLER software for comparative protein structure modeling.
Developing and automating a protocol for protein model construction.
Evaluating the accuracy of generated protein models.

Main Results:

A comparative model was successfully constructed for a protein of unknown structure using MODELLER.
Automated protocols yielded models of useful accuracy.
The method proved effective for over 50% of all known protein sequences.

Conclusions:

Computational modeling, specifically using MODELLER, effectively bridges the protein sequence-structure gap.
Automated protein structure modeling offers a scalable solution for characterizing large numbers of protein sequences.
The developed protocol provides valuable structural insights for a significant portion of the proteome.