ArticleStructure (London, England : 1993)2011
Automated prediction of protein association rate constants.
Article in Structure (London, England : 1993), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 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
75 citing papers in PubMed.
- Quantitative Modeling of TLR Signaling Reveals Missing Negative Feedback Guiding Identification of TANK-IKKε Checkpoint.bioRxiv : the preprint server for biology · 2026Article
- Biomathematical enzyme kinetics model of prebiotic autocatalytic RNA networks: degenerating parasite-specific hyperparasite catalysts confer parasite resistance and herald the birth of molecular immunity.PLoS computational biology · 2025Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies.Methods in molecular biology (Clifton, N.J.) · 2024Article
- RNA binding induces an allosteric switch in Cyp33 to repress MLL1-mediated transcription.Science advances · 2023Article
- Absolute protein quantitation of the mouse macrophage Toll-like receptor and chemotaxis pathways.Scientific data · 2022Article
- Spatial organization of hydrophobic and charged residues affects protein thermal stability and binding affinity.Scientific reports · 2022Article
- Cooperative stability renders protein complex formation more robust and controllable.Scientific reports · 2022Article
- Preferential Interactions of a Crowder Protein with the Specific Binding Site of a Native Protein Complex.The journal of physical chemistry letters · 2022Article
- Prediction of Protein-Protein Binding Affinities from Unbound Protein Structures.Methods in molecular biology (Clifton, N.J.) · 2022Review
- A novel computational strategy for defining the minimal protein molecular surface representation.PloS one · 2022Article
- Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions.The Biochemical journal · 2021Article
- Understanding the Targeting Mechanisms of Multi-Specific Biologics in Immunotherapy with Multiscale Modeling.iScience · 2020Article
- ISLAND: in-silico proteins binding affinity prediction using sequence information.BioData mining · 2020Article
- Using collections of structural models to predict changes of binding affinity caused by mutations in protein-protein interactions.Protein science : a publication of the Protein Society · 2020Article
- Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein-Protein Association.Biomolecules · 2020Article
- Disordered proteins follow diverse transition paths as they fold and bind to a partner.Science (New York, N.Y.) · 2020Article
- A Systematic Test of Receptor Binding Kinetics for Ligands in Tumor Necrosis Factor Superfamily by Computational Simulations.International journal of molecular sciences · 2020Article
- A Collision Coupling Model Governs the Activation of Neuronal GIRK1/2 Channels by Muscarinic-2 Receptors.Frontiers in pharmacology · 2020Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The association rate constants (k(a)) of proteins with other proteins or other macromolecular targets are a fundamental biophysical property. Observed rate constants span over ten orders of magnitude, from 1 to 10(10) M(-1)s(-1). Protein association can be rate limited either by the diffusional approach of the subunits to form a transient complex, with near-native separation and orientation but without short-range native interactions, or by the subsequent conformational rearrangement to form the native complex. Our transient-complex theory showed promise in predicting k(a) in the diffusion-limited regime. Here, we develop it into a web server called TransComp (http://pipe.sc.fsu.edu/transcomp/) and report on the server's accuracy and robustness based on applications to over 100 protein complexes. We expect this server to be a valuable tool for systems biology applications and for kinetic characterization of protein-protein and protein-nucleic acid association in general.
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.