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Updated: Jun 29, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

Paul C Whitford¹, Jeffrey K Noel, Shachi Gosavi

¹Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, California 92093, USA.

|October 7, 2008

Summary

This study explores protein folding mechanisms using an all-atom structure-based model. Findings reveal robust folding pathways and the significant impact of side chain packing and proline residues on protein dynamics.

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Last Updated: Jun 29, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

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Published on: July 25, 2013

Area of Science:

Biophysics
Computational Biology
Protein Dynamics

Background:

Protein dynamics occur across diverse timescales.
Coarse-grained models offer insights into long-range dynamics, while all-atom force fields provide high-resolution short-range dynamics.
Bridging these scales requires models with atomic detail.

Purpose of the Study:

To investigate the robustness of protein folding mechanisms using an all-atom structure-based model.
To explore the interplay between side chain packing and backbone folding.
To compare the all-atom model with C(alpha) models and empirical force fields.

Main Methods:

Development and application of an all-atom structure-based model.
Analysis of protein folding dynamics for specific protein domains (B domain of Protein A, SH3 domain, Chymotrypsin Inhibitor 2).
Comparison with C(alpha) structure-based and all-atom empirical force field models.

Main Results:

Backbone collapse and side chain packing occur cooperatively, with residual packing dependent on temperature.
Protein folding mechanisms demonstrate robustness to energetic parameter variations.
Folding free-energy barriers are tunable via parameter modifications.
Global folding mechanisms align between C(alpha) and all-atom models, with discrepancies due to energetic heterogeneity.
Proline residues significantly influence folding mechanisms, irrespective of isomerization.

Conclusions:

The all-atom structure-based model provides atomic resolution for studying protein folding.
Folding mechanisms are robust and can be modulated by energetic factors.
This model serves as a foundation for future research into energetic contributions to protein folding and function.