Predictive Modeling and Structure Analysis of Genetic Variants in Familial Hypercholesterolemia: Implications for Diagnosis and Protein Interaction Studies

Applications of artificial intelligence in clinical laboratory genomics

(2023) Swaroop Aradhya et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

Combination of expert guidelines-based and machine learning-based approaches leads to superior accuracy of automated prediction of clinical effect of copy number variations

(2023) Tomáš Sládeček et al.   Scientific Reports

Can AlphaFold2 predict the impact of missense mutations on structure?

(2022) Gwen R. Buel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Scoping review and classification of deep learning in medical genetics

(2022) Suzanna E. Ledgister Hanchard et al.   GENETICS IN MEDICINE

Classification of non-coding variants with high pathogenic impact

(2022) Lambert Moyon et al.   PLoS Genetics

Clinical Applications of Artificial Intelligence—An Updated Overview

(2022) Ștefan Busnatu et al.   Journal of Clinical Medicine

LDLR missense variants disturb structural conformation and LDLR activity in T-lymphocytes of Familial hypercholesterolemia patients

(2022) Thais Kristini Almendros Barbosa et al.   GENE

A structural biology community assessment of AlphaFold2 applications

(2022) Mehmet Akdel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Insights on variant analysis in silico tools for pathogenicity prediction

(2022) Felipe Antonio de Oliveira Garcia et al.   Frontiers in Genetics

MVP predicts the pathogenicity of missense variants by deep learning

(2021) Hongjian Qi et al.   Nature Communications

ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities

(2021) Jaie Woodard et al.   JOURNAL OF MOLECULAR BIOLOGY

Improved pathogenicity prediction for rare human missense variants

(2021) Yingzhou Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Using machine learning approaches for multi-omics data analysis: A review

(2021) Parminder S. Reel et al.   BIOTECHNOLOGY ADVANCES

Deep Learning-Based Advances in Protein Structure Prediction

(2021) Subash C. Pakhrin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Protein Structure Prediction: Conventional and Deep Learning Perspectives

(2021) V. A. Jisna et al.   PROTEIN JOURNAL

Assessment of the CASP14 assembly predictions

(2021) Burcu Ozden et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Machine learning in protein structure prediction

(2021) Mohammed AlQuraishi   CURRENT OPINION IN CHEMICAL BIOLOGY

The Clinical Genome Resource (ClinGen) Familial Hypercholesterolemia Variant Curation Expert Panel consensus guidelines for LDLR variant classification

(2021) Joana R. Chora et al.   GENETICS IN MEDICINE

A Systematic Approach to Assess the Activity and Classification of PCSK9 Variants

(2021) Kepa B. Uribe et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Protein–Protein Docking: Past, Present, and Future

(2021) Sharon Sunny et al.   PROTEIN JOURNAL

Sickle cell anemia: hierarchical cluster analysis and clinical profile in a cohort in Brazil

(2021) Valéria de Freitas Dutra et al.   Hematology Transfusion and Cell Therapy

An Introduction to Machine Learning

(2020) Solveig Badillo et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

In Silico Insights into Protein–Protein Interaction Disruptive Mutations in the PCSK9-LDLR Complex

(2020) William R. Martin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Macromolecular modeling and design in Rosetta: recent methods and frameworks

(2020) Julia Koehler Leman et al.   NATURE METHODS

Assessing performance of pathogenicity predictors using clinically relevant variant datasets

(2020) Adam C Gunning et al.   JOURNAL OF MEDICAL GENETICS

DynaMut2 : Assessing changes in stability and flexibility upon single and multiple point missense mutations

(2020) Carlos H.M. Rodrigues et al.   PROTEIN SCIENCE

Genomics, epigenomics and pharmacogenomics of familial hypercholesterolemia (FHBGEP): A study protocol

(2020) Jéssica Bassani Borges et al.   Research in Social & Administrative Pharmacy

Progress in finding pathogenic DNA copy number variations in dyslipidemia

(2019) Michael A. Iacocca et al.   CURRENT OPINION IN LIPIDOLOGY

FoldX 5.0: Working with RNA, small molecules and a new graphical interface

(2019) Javier Delgado et al.   BIOINFORMATICS

AlphaFold at CASP13

(2019) Mohammed AlQuraishi   BIOINFORMATICS

What method to use for protein–protein docking?

(2019) Kathryn A Porter et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein–protein interactions

(2019) Ankit A Roy et al.   NUCLEIC ACIDS RESEARCH

Deep‐learning contact‐map guided protein structure prediction in CASP13

(2019) Wei Zheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Estimation of model accuracy in CASP13

(2019) Jianlin Cheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Distance-based protein folding powered by deep learning

(2019) Jinbo Xu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Critical assessment of methods of protein structure prediction (CASP)—Round XIII

(2019) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Validation of LDLr Activity as a Tool to Improve Genetic Diagnosis of Familial Hypercholesterolemia: A Retrospective on Functional Characterization of LDLr Variants

(2018) Asier Benito-Vicente et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

The complex molecular genetics of familial hypercholesterolaemia

(2018) Amanda J. Berberich et al.   Nature Reviews Cardiology

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Toward Integrative Bayesian Analysis in Molecular Biology

(2018) Katja Ickstadt et al.   Annual Review of Statistics and Its Application

Deep learning in omics: a survey and guideline

(2018) Zhiqiang Zhang et al.   Briefings in Functional Genomics

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Systematic prediction of familial hypercholesterolemia caused by low-density lipoprotein receptor missense mutations

(2018) Jiayan Guo et al.   ATHEROSCLEROSIS

Low-density lipoproteins cause atherosclerotic cardiovascular disease. 1. Evidence from genetic, epidemiologic, and clinical studies. A consensus statement from the European Atherosclerosis Society Consensus Panel

(2017) Brian A. Ference et al.   EUROPEAN HEART JOURNAL

Analysis of publicly available LDLR, APOB, and PCSK9 variants associated with familial hypercholesterolemia: application of ACMG guidelines and implications for familial hypercholesterolemia diagnosis

(2017) Joana Rita Chora et al.   GENETICS IN MEDICINE

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

Points of Significance: Ensemble methods: bagging and random forests

(2017) Naomi Altman et al.   NATURE METHODS

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

Evaluation of the template-based modeling in CASP12

(2017) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

HawkRank: a new scoring function for protein–protein docking based on weighted energy terms

(2017) Ting Feng et al.   Journal of Cheminformatics

Diagnosis of Familial Hypercholesterolemia: Table 1

(2016) Ishwarlal Jialal et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

(2016) Nilah M. Ioannidis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Pooling and expanding registries of familial hypercholesterolaemia to assess gaps in care and improve disease management and outcomes: Rationale and design of the global EAS Familial Hypercholesterolaemia Studies Collaboration

(2016) Antonio J. Vallejo-Vaz et al.   ATHEROSCLEROSIS SUPPLEMENTS

STRUM: structure-based prediction of protein stability changes upon single-point mutation

(2016) Lijun Quan et al.   BIOINFORMATICS

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

US physician practices for diagnosing familial hypercholesterolemia: data from the CASCADE-FH registry

(2016) Zahid S. Ahmad et al.   Journal of Clinical Lipidology

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1

(2016) A. Vangone et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation of the coarse-grained OPEP force field for protein-protein docking

(2016) Philipp Kynast et al.   BMC Biophysics

Mutation Drivers of Immunological Responses to Cancer

(2016) E. Porta-Pardo et al.   Cancer Immunology Research

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

(2015) Yongwook Choi et al.   BIOINFORMATICS

Multiple sequence alignment modeling: methods and applications

(2015) Maria Chatzou et al.   BRIEFINGS IN BIOINFORMATICS

Proprotein Convertase Subtilisin/Kexin Type 9 Inhibition

(2015) Nathalie Bergeron et al.   CIRCULATION

The importance of an integrated analysis of clinical, molecular and functional data for the genetic diagnosis of familial hypercholesterolemia

(2015) Asier Benito-Vicente et al.   GENETICS IN MEDICINE

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

(2015) Sue Richards et al.   GENETICS IN MEDICINE

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

(2015) Thom Vreven et al.   JOURNAL OF MOLECULAR BIOLOGY

The Contribution of Missense Mutations in Core and Rim Residues of Protein–Protein Interfaces to Human Disease

(2015) Alessia David et al.   JOURNAL OF MOLECULAR BIOLOGY

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

ClinGen — The Clinical Genome Resource

(2015) Heidi L. Rehm et al.   NEW ENGLAND JOURNAL OF MEDICINE

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

(2015) C. Dong et al.   HUMAN MOLECULAR GENETICS

CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts

(2014) E. Chermak et al.   BIOINFORMATICS

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

Cancer3D: understanding cancer mutations through protein structures

(2014) Eduard Porta-Pardo et al.   NUCLEIC ACIDS RESEARCH

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

(2014) K. Khafizov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution

(2013) Jessica Andreani et al.   BIOINFORMATICS

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring

(2013) Brian Jiménez-García et al.   BIOINFORMATICS

Familial hypercholesterolaemia is underdiagnosed and undertreated in the general population: guidance for clinicians to prevent coronary heart disease: Consensus Statement of the European Atherosclerosis Society

(2013) B. G. Nordestgaard et al.   EUROPEAN HEART JOURNAL

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

Novel functional APOB mutations outside LDL-binding region causing familial hypercholesterolaemia

(2013) Ana Catarina Alves et al.   HUMAN MOLECULAR GENETICS

Identification and biochemical analysis of a novelAPOBmutation that causes autosomal dominant hypercholesterolemia

(2013) Ellen R. A. Thomas et al.   Molecular Genetics & Genomic Medicine

Identification and characterization of new gain-of-function mutations in the PCSK9 gene responsible for autosomal dominant hypercholesterolemia

(2012) Marianne Abifadel et al.   ATHEROSCLEROSIS

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field

(2012) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

Proprotein convertase subtilisin/kexin type 9 (PCSK9): From structure–function relation to therapeutic inhibition

(2011) G. Tibolla et al.   NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES

Three-Dimensional cryoEM Reconstruction of Native LDL Particles to 16Å Resolution at Physiological Body Temperature

(2011) Vibhor Kumar et al.   PLoS One

Using SIFT and PolyPhen to Predict Loss-of-Function and Gain-of-Function Mutations

(2010) Sarah E. Flanagan et al.   Genetic Testing and Molecular Biomarkers

Protein–protein docking tested in blind predictions: the CAPRI experiment

(2010) Joël Janin   Molecular BioSystems

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding

(2010) Carles Pons et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

(2010) Doron Betel et al.   GENOME BIOLOGY

Apolipoprotein B levels, APOB alleles, and risk of ischemic cardiovascular disease in the general population, a review

(2009) Marianne Benn   ATHEROSCLEROSIS

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Degradation of LDLR protein mediated by ‘gain of function’ PCSK9 mutants in normal and ARH cells

(2008) Tommaso Fasano et al.   ATHEROSCLEROSIS

PCSK9: An enigmatic protease

(2008) Dayami Lopez   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Contribution of Macromolecular Structure to the Retention of Low-Density Lipoprotein at Arterial Branch Points

(2008) Gina P. Kwon et al.   CIRCULATION

Recent Progress and Future Directions in Protein-Protein Docking

(2008) David Ritchie   CURRENT PROTEIN & PEPTIDE SCIENCE

Structural and Biochemical Characterization of the Wild Type PCSK9-EGF(AB) Complex and Natural Familial Hypercholesterolemia Mutants

(2008) Matthew J. Bottomley et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

FireDock: a web server for fast interaction refinement in molecular docking

(2008) E. Mashiach et al.   NUCLEIC ACIDS RESEARCH

Familial hypercholesterolaemia in Portugal

(2007) M. Bourbon et al.   ATHEROSCLEROSIS

Identification and characterization of two non-secreted PCSK9 mutants associated with familial hypercholesterolemia in cohorts from New Zealand and South Africa

(2007) Vivienne M. Homer et al.   ATHEROSCLEROSIS

Common and Rare Alleles in Apolipoprotein B Contribute to Plasma Levels of Low-Density Lipoprotein Cholesterol in the General Population

(2007) Marianne Benn et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM