Additivity principles in biochemistry.
Open accessAbstract
We cannot yet reliably fold proteins or RNA molecules by computer, predict ligand binding affinities, compute conformational transitions, or use the sequence information in the Human Genome very effectively to understand biomolecular function and disease. Why not? Perhaps some of our models in computational biology are based on flawed assumptions. Thermodynamic additivity principles are the foundations of chemistry, but few additivity principles have yet been found successful in biochemistry.
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The advantage of nonlinear scoring functions partially circumvents the problematic modeling assumptions of linear models.
“This advantage of nonlinear scoring functions partially circumvents the problematic modeling assumptions of linear models (Dill, 1997; Baum et al., 2010; Sotriffer, 2012).”
From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Dill, 1997
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References 47 · Cited by 347
- Authors
- Dill, K. A.
- Affiliations
- University of California, San Francisco (US)
- Corresponding author
- Dill, Ken A.
- ORCID
- Dill, Ken A.
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 1997-01
- Volume
- 272
- Issue
- 2
- Pages
- 701-704
- ISSN
- 0021-9258 (ISSN-L)
- OpenAlex
- W2123768455
- Cited by
- 347
- References
- 47
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 7 · 2023: 5 · 2022: 11 · 2021: 12 · 2020: 5 · 2019: 12 · 2018: 8 · 2017: 8 · 2016: 15 · 2015: 11 · 2014: 9 · 2013: 17 · 2012: 19
- FWCI
- 2.12
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › thermodynamics and calorimetric analyses
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- additivity rule, protein folding, RNA folding, ligand binding affinity prediction, conformational change, biomolecular function
- MeSH terms
- Animals, Biochemical Phenomena, Biochemistry, Models, Biological, Thermodynamics, Entropy
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