ArticleJournal of molecular modeling2009
Solvent accessible surface area approximations for rapid and accurate protein structure prediction.
Article in Journal of molecular modeling, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 179 papers.
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Who cites it
179 citing papers in PubMed, 442 citations in OpenAlex.
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- AlphaInterp: Mechanistic Interpretability of AlphaFold 3 Reveals How Evolutionary Information Shapes Protein Structure Prediction.bioRxiv : the preprint server for biology · 2026Article
- Precise discrimination of G-quadruplex conformation by chiral nanoassembly with photo-reversibility.Nature communications · 2026Article
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119 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The burial of hydrophobic amino acids in the protein core is a driving force in protein folding. The extent to which an amino acid interacts with the solvent and the protein core is naturally proportional to the surface area exposed to these environments. However, an accurate calculation of the solvent-accessible surface area (SASA), a geometric measure of this exposure, is numerically demanding as it is not pair-wise decomposable. Furthermore, it depends on a full-atom representation of the molecule. This manuscript introduces a series of four SASA approximations of increasing computational complexity and accuracy as well as knowledge-based environment free energy potentials based on these SASA approximations. Their ability to distinguish correctly from incorrectly folded protein models is assessed to balance speed and accuracy for protein structure prediction. We find the newly developed "Neighbor Vector" algorithm provides the most optimal balance of accurate yet rapid exposure measures.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.