# The range of the contact interactions and the kinetics of the Go models of proteins

Source: [The range of the contact interactions and the kinetics of the Go models of proteins](<https://www.sota2.com/research/paper/68fa25b02c2a3760193b2cab>)

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

Data updated: 2025-10-24T10:53:25.022Z

Authors: Marek Cieplak, Trinh Xuan Hoang

Published: 2002-06-16T18:39:55.000Z

## Abstract

We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R\_c$, between the C$\_\\alpha$ atoms. The folding times depend on the value of $R\_c$ strongly and non-monotonically due to the interplay between frustration and the free energy barrier for folding. This indicates a need for a physically determined set of native contacts that takes into account all the residual atoms. %%. One may accomplish it This can be accomplished by considering the van der Waals radii of the atoms and checking if %%the atoms overlap. they are found within a proper range of the van der Waals attraction. In the second model, non-native attractive contacts are added to the system. This leads to bad foldability. However, for a small number of such extra contacts there is a slight acceleration in the kinetics of folding.

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/cond-mat/0206299>)

[PDF](<https://arxiv.org/pdf/cond-mat/0206299.pdf>)