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References from Using AI-predicted protein structures as a reference to predict loss-of-function activity in tumor suppressor breast cancer genes. Local targets link to admitted publications; unresolved targets remain external evidence.
A population-based study of genes previously implicated in breast cancer
10.1056/nejmoa2005936 · 2021 · External reference
ClinVar: improving access to variant interpretations and supporting evidence
10.1093/nar/gkx1153 · 2018 · External reference
Identifying Mendelian disease genes with the variant effect scoring tool
10.1186/1471-2164-14-s3-s3 · 2013 · External reference
Predicting functional effect of human missense mutations using PolyPhen-2
10.1002/0471142905.hg0720s76 · 2013 · External reference
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American college of medical genetics and genomics and the association for molecular pathology
10.1038/gim.2015.30 · 2015 · External reference
Loss of protein structure stability as a major causative factor in monogenic disease
10.1016/j.jmb.2005.08.020 · 2005 · External reference
Identification of pathogenic missense mutations using protein stability predictors
10.1038/s41598-020-72404-w · 2020 · External reference
Analysis and interpretation of the impact of missense variants in cancer
10.3390/ijms22115416 · 2021 · External reference
BRCA1 haploinsufficiency: consequences for breast cancer
2012 · External reference
BRCA2 haploinsufficiency in telomere maintenance
10.3390/genes13010083 · 2021 · External reference
Rad51C is essential for embryonic development and haploinsufficiency causes increased DNA damage sensitivity and genomic instability
2010 · External reference
Heterozygous mutations in PALB2 cause DNA replication and damage response defects
10.1038/ncomms3578 · 2013 · External reference
FoldX 5.0: working with RNA, small molecules and a new graphical interface
10.1093/bioinformatics/btz184 · 2019 · External reference
The Rosetta all-atom energy function for macromolecular modeling and design
10.1021/acs.jctc.7b00125 · 2017 · External reference
DDGun: an untrained predictor of protein stability changes upon amino acid variants
10.1093/nar/gkac325 · 2022 · External reference
Correspondence between functional scores from deep mutational scans and predicted effects on protein stability
10.1002/pro.4688 · 2023 · External reference
Control of protein stability by post-translational modifications
10.1038/s41467-023-35795-8 · 2023 · External reference
Protein Stability Perturbation Contributes to the Loss of Function in Haploinsufficient Genes
10.3389/fmolb.2021.620793 · 2021 · External reference
Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset
2022 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Evolutionary-scale prediction of atomic-level protein structure with a language model
10.1126/science.ade2574 · 2023 · External reference
The transformative power of transformers in protein structure prediction
10.1073/pnas.2303499120 · 2023 · External reference
Improved protein structure prediction using potentials from deep learning
10.1038/s41586-019-1923-7 · 2020 · External reference
Applying and improving AlphaFold at CASP14,"
10.1002/prot.26257 · 2021 · External reference
Predicting the pathogenicity of missense variants using features derived from AlphaFold2
10.1093/bioinformatics/btad280 · 2023 · External reference
10.1016/j.csbj.2022.11.048 · 2023 · Admitted local publication
Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures
2022 · External reference
The power of multiplexed functional analysis of genetic variants
10.1038/nprot.2016.135 · 2016 · External reference
Accurate classification of BRCA1 variants with saturation genome editing
10.1038/s41586-018-0461-z · 2018 · External reference
Functional analysis and clinical classification of 462 germline BRCA2 missense variants affecting the DNA binding domain
10.1016/j.ajhg.2024.02.002 · 2024 · External reference
Functional and clinical characterization of variants of uncertain significance identifies a hotspot for inactivating missense variants in RAD51C
10.1158/0008-5472.can-22-2319 · 2023 · External reference
Functional characterization of 84 PALB2 variants of uncertain significance
10.1038/s41436-019-0682-z · 2020 · External reference
Functional analysis of genetic variants in the high-risk breast cancer susceptibility gene PALB2
10.1038/s41467-019-13194-2 · 2019 · External reference
Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the association for molecular pathology, American society of clinical oncology, and college of american pathologists
10.1016/j.jmoldx.2016.10.002 · 2017 · External reference
REVEL: an ensemble method for predicting the pathogenicity of rare missense variants
10.1016/j.ajhg.2016.08.016 · 2016 · External reference
PERCH: a unified framework for disease gene prioritization
10.1002/humu.23158 · 2017 · External reference
REVEL and bayesdel outperform other in silico meta-predictors for clinical variant classification
10.1038/s41598-019-49224-8 · 2019 · External reference
Accurate proteome-wide missense variant effect prediction with AlphaMissense
10.1126/science.adg7492 · 2023 · External reference
MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning
10.1186/s13073-022-01120-z · 2022 · External reference
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs
10.1186/s13073-020-00803-9 · 2020 · External reference
Peptide library approach to uncover phosphomimetic inhibitors of the BRCA1C-terminal domain
10.1021/cb500757u · 2015 · External reference
Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1
10.1038/nsb1001-838 · 2001 · External reference
Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer
10.1038/nsmb775 · 2004 · External reference
Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation
10.1038/s41586-021-03716-8 · 2021 · External reference
BRCA2 Function in DNA Binding and Recombination from a BRCA2-DSS1-ssDNA structure
10.1126/science.297.5588.1837 · 2002 · External reference
Structural insights into BCDX2 complex function in homologous recombination
10.1038/s41586-023-06219-w · 2023 · External reference
Structure and function of the RAD51B-RAD51C-RAD51D-XRCC2 tumour suppressor
10.1038/s41586-023-06179-1 · 2023 · External reference
Structural basis for recruitment of BRCA2 by PALB2
10.1038/embor.2009.126 · 2009 · External reference
ColabFold: making protein folding accessible to all
10.1038/s41592-022-01488-1 · 2022 · External reference
Biopython: freely available Python tools for computational molecular biology and bioinformatics
10.1093/bioinformatics/btp163 · 2009 · External reference
pyFoldX: enabling biomolecular analysis and engineering along structural ensembles
10.1093/bioinformatics/btac072 · 2022 · External reference
Simultaneous optimization of biomolecular energy functions on features from small molecules and macromolecules
10.1021/acs.jctc.6b00819 · 2016 · External reference
Predicting and interpreting large-scale mutagenesis data using analyses of protein stability and conservation
10.1016/j.celrep.2021.110207 · 2022 · External reference
SciPy 1.0—fundamental algorithms for scientific computing in python
10.1038/s41592-019-0686-2 · 2020 · External reference
Scikit-learn: machine learning in python
2011 · External reference
Methods of protein structure comparison
2012 · External reference
The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity
10.1002/humu.22768 · 2015 · External reference
