ArticlePLoS computational biology2012
Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 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
- Thermodynamics and Kinetics of Supramolecular Complex Formation between Carboxymethylcellulose and Lactoferrin.ACS omega · 2026Article
- Allosteric inhibition of the IZUMO1-JUNO fertilization complex by the naturally occurring antisperm antibody OBF13.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Computational Assessment of Protein-protein Binding Affinity by Reversely Engineering the Energetics in Protein Complexes.Genomics, proteomics & bioinformatics · 2021Article
- Classification of protein-protein association rates based on biophysical informatics.BMC bioinformatics · 2021Article
- Understanding the Impacts of Conformational Dynamics on the Regulation of Protein-Protein Association by a Multiscale Simulation Method.Journal of chemical theory and computation · 2020Article
- Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein-Protein Association.Biomolecules · 2020Article
- Multiscale simulation unravel the kinetic mechanisms of inflammasome assembly.Biochimica et biophysica acta. Molecular cell research · 2020Article
- A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- KOFFI and Anabel 2.0-a new binding kinetics database and its integration in an open-source binding analysis software.Database : the journal of biological databases and curation · 2019Article
- Application of targeted mass spectrometry in bottom-up proteomics for systems biology research.Journal of proteomics · 2018Review
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures.Bioinformatics (Oxford, England) · 2018Article
- Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.Scientific reports · 2017Article
- Unfair competition governs the interaction of pCPI-17 with myosin phosphatase (PP1-MYPT1).eLife · 2017Article
- A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison.Proteins · 2017Article
- Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics.Journal of chemical information and modeling · 2016Article
- Article
- Towards structural systems pharmacology to study complex diseases and personalized medicine.PLoS computational biology · 2014Review
- Modeling protein association mechanisms and kinetics.Current opinion in structural biology · 2013Review
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
The prediction of protein-protein kinetic rate constants provides a fundamental test of our understanding of molecular recognition, and will play an important role in the modeling of complex biological systems. In this paper, a feature selection and regression algorithm is applied to mine a large set of molecular descriptors and construct simple models for association and dissociation rate constants using empirical data. Using separate test data for validation, the predicted rate constants can be combined to calculate binding affinity with accuracy matching that of state of the art empirical free energy functions. The models show that the rate of association is linearly related to the proportion of unbound proteins in the bound conformational ensemble relative to the unbound conformational ensemble, indicating that the binding partners must adopt a geometry near to that of the bound prior to binding. Mirroring the conformational selection and population shift mechanism of protein binding, the models provide a strong separate line of evidence for the preponderance of this mechanism in protein-protein binding, complementing structural and theoretical studies.
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.