# Discrete molecular dynamics studies of the folding of a protein-like model

Source: [Discrete molecular dynamics studies of the folding of a protein-like model](<https://www.sota2.com/research/paper/68fa1eab7a2b558e29323dac>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-23T17:06:32.971Z

Authors: Nikolay V. Dokholyan, Sergey V. Buldyrev, H. Eugene Stanley, Eugene I. Shakhnovich (2) \_\_INSTITUTION\_4\_\_ Center for Polymer Studies, Physics Department, Boston University, Boston, (2) Department of Chemistry, Harvard University, Cambridge)

Published: 1998-12-17T02:15:13.000Z

## Abstract

Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical properties of the proteins (lattice models), while others are computationally heavy (traditional MD).   Results: We use a recently-proposed approach of Zhou and Karplus to study the folding of the protein model based on the discrete time molecular dynamics algorithm. We show that this algorithm resolves with respect to time the folding --- unfolding transition. In addition, we demonstrate the ability to study the coreof the model protein.   Conclusion: The algorithm along with the model of inter-residue interactions can serve as a tool to study the thermodynamics and kinetics of protein models.

## Recorded benchmark results

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/cond-mat/9812291>)

[PDF](<https://arxiv.org/pdf/cond-mat/9812291.pdf>)