ArticleProteins2013
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
Article in Proteins, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 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
53 citing papers in PubMed, 93 citations in OpenAlex.
- 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
- Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity inNAR genomics and bioinformatics · 2024Article
- Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.Proteins · 2023Article
- Quantification of biases in predictions of protein-protein binding affinity changes upon mutations.Briefings in bioinformatics · 2023Article
- Design of protein-binding peptides with controlled binding affinity: the case of SARS-CoV-2 receptor binding domain and angiotensin-converting enzyme 2 derived peptides.Frontiers in molecular biosciences · 2023Article
- Article
- Protein-protein interaction prediction methods: from docking-based to AI-based approaches.Biophysical reviews · 2022Review
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Article
- Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets.Frontiers in molecular biosciences · 2021Article
- SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function.Bioinformatics (Oxford, England) · 2020Article
- A novel strategy for molecular interfaces optimization: The case of Ferritin-Transferrin receptor interaction.Computational and structural biotechnology journal · 2020Article
- Article
- SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.Bioinformatics (Oxford, England) · 2019Article
- DisruPPI: structure-based computational redesign algorithm for protein binding disruption.Bioinformatics (Oxford, England) · 2018Article
- HawkRank: a new scoring function for protein-protein docking based on weighted energy terms.Journal of cheminformatics · 2017Article
- Computational Studies of Snake Venom Toxins.Toxins · 2017Review
- Systematic Identification of Machine-Learning Models Aimed to Classify Critical Residues for Protein Function from Protein Structure.Molecules (Basel, Switzerland) · 2017Article
- Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins.Scientific reports · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
70 authors at 20 institutions in 13 countries.
Funding
Abstract
Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies.
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.