2026-06-28T04:55:06Zhttps://docta.ucm.es/rest/oai/requestoai:docta.ucm.es:20.500.14352/926332024-08-01T00:04:06Zcom_20.500.14352_14col_20.500.14352_15
Docta Complutense
author
Sancho, David de
author
Rey Gayo, Antonio
2024-01-11T18:05:58Z
2024-01-11T18:05:58Z
2007
De Sancho, D. and Rey, A. (2007), Evaluation of coarse grained models for hydrogen bonds in proteins. J. Comput. Chem., 28: 1187-1199. https://doi.org/10.1002/jcc.20619
0192-8651
10.1002/jcc.20619
https://hdl.handle.net/20.500.14352/92633
1096-987X
https://doi.org/10.1002/jcc.20619
Backbone hydrogen bonds contribute very importantly to the stability of proteins and therefore they must be appropriately represented in protein folding simulations. Simple models are frequently used in theoretical approaches to this process, but their simplifications are often confronted with the need to be true to the physics of the interactions. Here we study the effects of different levels of coarse graining in the modeling of backbone hydrogen bonds. We study three different models taken from the bibliography in a twofold fashion. First, we calculate the hydrogen bonds in 2gb1, an (α + β)‐protein, and see how different backbone representations and potentials can mimic the effects of real hydrogen bonds both in helices and sheets. Second, we use an evolutionary method for protein fragment assembly to locate the global energy minimum for a set of small β‐proteins with these models. This way, we assess the effects of coarse graining in hydrogen bonding models and show what can be expected from them when used in simulation experiments.
eng
Evaluation of coarse grained models for hydrogen bonds in proteins
journal article
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Evaluation_of_coarse_grained_models.pdf