ArticleMethods (San Diego, Calif.)2010
Computing free energies of protein conformations from explicit solvent simulations.
Article in Methods (San Diego, Calif.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Testing the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein.Biophysical journal · 2024Article
- Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation.Biophysical journal · 2013Article
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Authors and funding
5 authors.
Funding
Abstract
We report a fully general technique addressing a long standing challenge of calculating conformational free energy differences between various states of a polymer chain from simulations using explicit solvent force fields. The main feature of our method is a special mapping variable, a path coordinate, which continuously connects two conformations. The path variable has been designed to preserve locality in the phase space near the path endpoints. We avoid the problem of sampling the unfolded states by creating an artificial confinement "tube" in the phase space that prevents the molecule from unfolding without affecting the calculation of the desired free energy difference. We applied our technique to compute the free energy difference between two native-like conformations of the small protein Trp-cage using the CHARMM force field with explicit solvent. We verified this result by comparing it with an independent, significantly more expensive calculation. Overall, the present study suggests that the new method of computing free energy differences between polymer chain conformations is accurate and highly computationally efficient.
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