ArticleJournal of the American Chemical Society2016
Finding Our Way in the Dark Proteome.
Article in Journal of the American Chemical Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- Mapping the functional dark proteome in cancer.Nature reviews. Cancer · 2026Review
- Shining light on the dark proteome with unstructural biology.Current research in structural biology · 2026Article
- IDPForge: Deep Learning of Proteins with Global and Local Regions of Disorder.bioRxiv : the preprint server for biology · 2026Article
- Accurate conformational ensembles of intrinsically disordered proteins using reweighting based on NMR chemical shifts.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- From CASP13 to the Nobel Prize: DeepMind's AlphaFold Journey in Revolutionizing Protein Structure Prediction and Beyond.Current protein & peptide science · 2026Review
- AlphaFlex: Ensembles of the human proteome representing disordered regions.bioRxiv : the preprint server for biology · 2025Article
- Quality Evaluation Based Simulation Selection (QEBSS) for analysis of conformational ensembles and dynamics of multidomain proteins.Communications chemistry · 2025Article
- Structural investigations connect the disordered N-terminal extension of HypB to the activities of HypB and SlyD in E. coli.Protein science : a publication of the Protein Society · 2025Article
- Decoding biomolecular condensate dynamics: an energy landscape approach.PLoS computational biology · 2025Article
- Prediction of Disordered Linkers Using APOD.Methods in molecular biology (Clifton, N.J.) · 2025Article
- UCBShift 2.0: Bridging the Gap from Backbone to Side Chain Protein Chemical Shift Prediction for Protein Structures.Journal of the American Chemical Society · 2024Article
- Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes.ArXiv · 2024Article
- A curated rotamer library for common post-translational modifications of proteins.Bioinformatics (Oxford, England) · 2024Article
- Article
- Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins.Current opinion in structural biology · 2024Review
- Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Learning to evolve structural ensembles of unfolded and disordered proteins using experimental solution data.The Journal of chemical physics · 2023Article
- The Role of Transient Intermediate Structures in the Unfolding of the Trp-Cage Fast-Folding Protein: Generating Ensembles from Time-Resolved X-ray Solution Scattering with Genetic Algorithms.The journal of physical chemistry letters · 2023Article
- NMR insights into dynamic, multivalent interactions of intrinsically disordered regions: from discrete complexes to condensates.Essays in biochemistry · 2022Article
- AlphaFold2 models indicate that protein sequence determines both structure and dynamics.Scientific reports · 2022Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
The traditional structure-function paradigm has provided significant insights for well-folded proteins in which structures can be easily and rapidly revealed by X-ray crystallography beamlines. However, approximately one-third of the human proteome is comprised of intrinsically disordered proteins and regions (IDPs/IDRs) that do not adopt a dominant well-folded structure, and therefore remain "unseen" by traditional structural biology methods. This Perspective considers the challenges raised by the "Dark Proteome", in which determining the diverse conformational substates of IDPs in their free states, in encounter complexes of bound states, and in complexes retaining significant disorder requires an unprecedented level of integration of multiple and complementary solution-based experiments that are analyzed with state-of-the art molecular simulation, Bayesian probabilistic models, and high-throughput computation. We envision how these diverse experimental and computational tools can work together through formation of a "computational beamline" that will allow key functional features to be identified in IDP structural ensembles.
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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.