ArticleProceedings of the National Academy of Sciences of the United States of America2012
Dominant folding pathways of a WW domain.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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
36 citing papers in PubMed.
- DreamFold: A World Model to efficiently generate protein folding pathways in the latent space.Protein science : a publication of the Protein Society · 2026Article
- Unveiling hidden intermediate states in protein folding with AI-based conditional transition clustering.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Mapping cryptic phosphorylation sites in the human proteome.The EMBO journal · 2025Article
- The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables.The journal of physical chemistry letters · 2025Article
- The evolution of eukaryotic linear motifs governing the function of androgen receptor from fish to Homo sapiens.Nucleic acids research · 2025Article
- Expanded Functionality and Portability for the Colvars Library.The journal of physical chemistry. B · 2024Article
- Information Bottleneck Approach for Markov Model Construction.Journal of chemical theory and computation · 2024Article
- Article
- An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes.Journal of chemical theory and computation · 2023Article
- New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain.The journal of physical chemistry. B · 2020Article
- Successes and challenges in simulating the folding of large proteins.The Journal of biological chemistry · 2020Review
- A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints.International journal of molecular sciences · 2019Article
- Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions.International journal of molecular sciences · 2018Article
- All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding.Biophysical journal · 2018Article
- Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation.FEBS letters · 2017Article
- Intrinsic map dynamics exploration for uncharted effective free-energy landscapes.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Finding multiple reaction pathways via global optimization of action.Nature communications · 2017Article
- High-Resolution Mapping of the Folding Transition State of a WW Domain.Journal of molecular biology · 2016Article
- Perspective: Computer simulations of long time dynamics.The Journal of chemical physics · 2016Article
- The Role of Electrostatic Interactions in Folding of β-Proteins.Journal of the American Chemical Society · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We investigate the folding mechanism of the WW domain Fip35 using a realistic atomistic force field by applying the Dominant Reaction Pathways approach. We find evidence for the existence of two folding pathways, which differ by the order of formation of the two hairpins. This result is consistent with the analysis of the experimental data on the folding kinetics of WW domains and with the results obtained from large-scale molecular dynamics simulations of this system. Free-energy calculations performed in two coarse-grained models support the robustness of our results and suggest that the qualitative structure of the dominant paths are mostly shaped by the native interactions. Computing a folding trajectory in atomistic detail only required about one hour on 48 Central Processing Units. The gain in computational efficiency opens the door to a systematic investigation of the folding pathways of a large number of globular proteins.
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.