ArticleProtein science : a publication of the Protein Society2008
Predicting protein folding rates from geometric contact and amino acid sequence.
Article in Protein science : a publication of the Protein Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed.
- Improving the Reliability of Protein Folding Rate Predictions by Applying Guidelines for Validating QSAR/QSPR Models.International journal of molecular sciences · 2026Article
- Rapid estimation of protein folding pathways from sequence alone using AlphaFold2.Nature communications · 2025Article
- Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design.Molecular biotechnology · 2025Review
- AlphaFold2bioRxiv : the preprint server for biology · 2024Article
- Fuzzy spherical truncation-based multi-linear protein descriptors: From their definition to application in structural-related predictions.Frontiers in chemistry · 2022Article
- Study on the Influence of mRNA, the Genetic Language, on Protein Folding Rates.Frontiers in genetics · 2021Article
- Stepwise optimization of recombinant protein production in Escherichia coli utilizing computational and experimental approaches.Applied microbiology and biotechnology · 2020Review
- The Molten Globule, and Two-State vs. Non-Two-State Folding of Globular Proteins.Biomolecules · 2020Review
- How Quickly Do Proteins Fold and Unfold, and What Structural Parameters Correlate with These Values?Biomolecules · 2020Article
- Tensor Algebra-based Geometrical (3D) Biomacro-Molecular Descriptors for Protein Research: Theory, Applications and Comparison with other Methods.Scientific reports · 2019Article
- Kinetic versus thermodynamic control of mutational effects on protein homeostasis: A perspective from computational modeling and experiment.Protein science : a publication of the Protein Society · 2019Article
- PFDB: A standardized protein folding database with temperature correction.Scientific reports · 2019Article
- Finding the needle in the haystack: towards solving the protein-folding problem computationally.Critical reviews in biochemistry and molecular biology · 2018Review
- Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins.Scientific reports · 2017Article
- Widespread position-specific conservation of synonymous rare codons within coding sequences.PLoS computational biology · 2017Article
- Role of Proteome Physical Chemistry in Cell Behavior.The journal of physical chemistry. B · 2016Review
- Rapidly Translated Polypeptides Are Preferred Substrates for Cotranslational Protein Degradation.The Journal of biological chemistry · 2016Article
- A prostate-specific antigen-dependent fusion polypeptide inhibits growth of prostate cancer cells in vitro and in vivo.American journal of cancer research · 2016Article
- Conformational sampling and structure prediction of multiple interacting loops in soluble and β-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method.Bioinformatics (Oxford, England) · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Protein folding speeds are known to vary over more than eight orders of magnitude. Plaxco, Simons, and Baker (see References) first showed a correlation of folding speed with the topology of the native protein. That and subsequent studies showed, if the native structure of a protein is known, its folding speed can be predicted reasonably well through a correlation with the "localness" of the contacts in the protein. In the present work, we develop a related measure, the geometric contact number, N (alpha), which is the number of nonlocal contacts that are well-packed, by a Voronoi criterion. We find, first, that in 80 proteins, the largest such database of proteins yet studied, N (alpha) is a consistently excellent predictor of folding speeds of both two-state fast folders and more complex multistate folders. Second, we show that folding rates can also be predicted from amino acid sequences directly, without the need to know the native topology or other structural properties.
Indexed as
Identifiers
What OpenQuestion holds
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.