Computational Approaches to Prioritize Cancer Driver Missense Mutations
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Title
Computational Approaches to Prioritize Cancer Driver Missense Mutations
Authors
Keywords
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Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 19, Issue 7, Pages 2113
Publisher
MDPI AG
Online
2018-07-23
DOI
10.3390/ijms19072113
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Note: Only part of the references are listed.- Dynamics and structural stability effects of germline PTEN mutations associated with cancer versus autism phenotypes
- (2018) Iris Nira Smith et al. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
- Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations
- (2018) David Tamborero et al. Genome Medicine
- A Novel p.Leu(381)Phe Mutation in Presenilin 1 is Associated with Very Early Onset and Unusually Fast Progressing Dementia as well as Lysosomal Inclusions Typically Seen in Kufs Disease
- (2018) Natalia Dolzhanskaya et al. JOURNAL OF ALZHEIMERS DISEASE
- DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding
- (2017) Lin Li et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer
- (2017) Malachi Griffith et al. NATURE GENETICS
- Comparison of algorithms for the detection of cancer drivers at subgene resolution
- (2017) Eduard Porta-Pardo et al. NATURE METHODS
- mCSM–NA: predicting the effects of mutations on protein–nucleic acids interactions
- (2017) Douglas E.V. Pires et al. NUCLEIC ACIDS RESEARCH
- Exploring background mutational processes to decipher cancer genetic heterogeneity
- (2017) Alexander Goncearenco et al. NUCLEIC ACIDS RESEARCH
- Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes
- (2017) Yunhui Peng et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations
- (2017) Lin Li et al. Scientific Reports
- Computing disease-linked SOD1 mutations: deciphering protein stability and patient-phenotype relations
- (2017) Vijay Kumar et al. Scientific Reports
- Adaptive patterns in the p53 protein sequence of the hypoxia- and cancer-tolerant blind mole rat Spalax
- (2016) Vered Domankevich et al. BMC EVOLUTIONARY BIOLOGY
- SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations
- (2016) Marharyta Petukh et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach
- (2016) Ivan Getov et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase
- (2016) Yunhui Peng et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Unsupervised detection of cancer driver mutations with parsimony-guided learning
- (2016) Runjun D Kumar et al. NATURE GENETICS
- Protein-structure-guided discovery of functional mutations across 19 cancer types
- (2016) Beifang Niu et al. NATURE GENETICS
- DoCM: a database of curated mutations in cancer
- (2016) Benjamin J Ainscough et al. NATURE METHODS
- StructMAn: annotation of single-nucleotide polymorphisms in the structural context
- (2016) Alexander Gress et al. NUCLEIC ACIDS RESEARCH
- MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions
- (2016) Minghui Li et al. NUCLEIC ACIDS RESEARCH
- Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding
- (2016) Yunhui Peng et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation
- (2016) Chien-Hao Chiang et al. Scientific Reports
- Towards a “Golden Standard” for computing globin stability: Stability and structure sensitivity of myoglobin mutants
- (2015) Kasper P. Kepp BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- MAESTRO - multi agent stability prediction upon point mutations
- (2015) Josef Laimer et al. BMC BIOINFORMATICS
- Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes
- (2015) Feixiong Cheng et al. BRIEFINGS IN BIOINFORMATICS
- Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation
- (2015) M. Li et al. CANCER RESEARCH
- Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2
- (2015) Tugba G. Kucukkal et al. Computational and Mathematical Methods in Medicine
- ‘Latent drivers’ expand the cancer mutational landscape
- (2015) Ruth Nussinov et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- On Human Disease-Causing Amino Acid Variants: Statistical Study of Sequence and Structural Patterns
- (2015) Marharyta Petukh et al. HUMAN MUTATION
- 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
- dSysMap: exploring the edgetic role of disease mutations
- (2015) Roberto Mosca et al. NATURE METHODS
- Comprehensive assessment of cancer missense mutation clustering in protein structures
- (2015) Atanas Kamburov et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
- (2015) Marharyta Petukh et al. PLoS Computational Biology
- Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles
- (2015) Jeffrey R. Brender et al. PLoS Computational Biology
- Mutant Cbl proteins as oncogenic drivers in myeloproliferative disorders
- (2015) Mayumi Naramura et al. Oncotarget
- A spatial simulation approach to account for protein structure when identifying non-random somatic mutations
- (2014) Gregory A Ryslik et al. BMC BIOINFORMATICS
- The structural network of Interleukin-10 and its implications in inflammation and cancer
- (2014) Ece Acuner-Ozbabacan et al. BMC GENOMICS
- NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation
- (2014) Manuel Giollo et al. BMC GENOMICS
- Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity
- (2014) Minghui Li et al. Journal of Chemical Theory and Computation
- Prospective Enterprise-Level Molecular Genotyping of a Cohort of Cancer Patients
- (2014) Laura E. MacConaill et al. JOURNAL OF MOLECULAR DIAGNOSTICS
- Computing Stability Effects of Mutations in Human Superoxide Dismutase 1
- (2014) Kasper P. Kepp JOURNAL OF PHYSICAL CHEMISTRY B
- R3P-Loc: A compact multi-label predictor using ridge regression and random projection for protein subcellular localization
- (2014) Shibiao Wan et al. JOURNAL OF THEORETICAL BIOLOGY
- Cancer3D: understanding cancer mutations through protein structures
- (2014) Eduard Porta-Pardo et al. NUCLEIC ACIDS RESEARCH
- HybridGO-Loc: Mining Hybrid Features on Gene Ontology for Predicting Subcellular Localization of Multi-Location Proteins
- (2014) Shibiao Wan et al. PLoS One
- Coverage of protein domain families with structural protein–protein interactions: Current progress and future trends
- (2014) Alexander Goncearenco et al. PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
- Kin-Driver: a database of driver mutations in protein kinases
- (2014) F. L. Simonetti et al. Database-The Journal of Biological Databases and Curation
- Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning
- (2014) Nan Zhao et al. PLoS Computational Biology
- All-Atom Molecular Dynamics Simulations of Actin–Myosin Interactions: A Comparative Study of Cardiac α Myosin, β Myosin, and Fast Skeletal Muscle Myosin
- (2013) Minghui Li et al. BIOCHEMISTRY
- Molecular modelling and simulations in cancer research
- (2013) Ran Friedman et al. BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
- Predicting the functional consequences of cancer-associated amino acid substitutions
- (2013) Hashem A. Shihab et al. BIOINFORMATICS
- mCSM: predicting the effects of mutations in proteins using graph-based signatures
- (2013) Douglas E. V. Pires et al. BIOINFORMATICS
- MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures
- (2013) Noushin Niknafs et al. HUMAN GENETICS
- 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
- A Y328C missense mutation in spermine synthase causes a mild form of Snyder–Robinson syndrome
- (2013) Zhe Zhang et al. HUMAN MOLECULAR GENETICS
- A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation
- (2013) Luigi Boccuto et al. HUMAN MOLECULAR GENETICS
- A Constitutively Activating Mutation Alters the Dynamics and Energetics of a Key Conformational Change in a Ligand-free G Protein-coupled Receptor
- (2013) Hisao Tsukamoto et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Mutations in DNA-Binding Loop of NFAT5 Transcription Factor Produce Unique Outcomes on Protein–DNA Binding and Dynamics
- (2013) Minghui Li et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A rational free energy-based approach to understanding and targeting disease-causing missense mutations
- (2013) Zhe Zhang et al. JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
- The Cancer Genome Atlas Pan-Cancer analysis project
- (2013) John N Weinstein et al. NATURE GENETICS
- Computational approaches to identify functional genetic variants in cancer genomes
- (2013) NATURE METHODS
- Interaction-based discovery of functionally important genes in cancers
- (2013) Dario Ghersi et al. NUCLEIC ACIDS RESEARCH
- BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations
- (2013) Yves Dehouck et al. NUCLEIC ACIDS RESEARCH
- ClinVar: public archive of relationships among sequence variation and human phenotype
- (2013) Melissa J. Landrum et al. NUCLEIC ACIDS RESEARCH
- Cancer Missense Mutations Alter Binding Properties of Proteins and Their Interaction Networks
- (2013) Hafumi Nishi et al. PLoS One
- CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features
- (2013) Yong Mao et al. PLoS One
- Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase
- (2013) L. Sutto et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- RAC1P29S is a spontaneously activating cancer-associated GTPase
- (2013) M. J. Davis et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
- (2013) J. Gao et al. Science Signaling
- Enhancing Human Spermine Synthase Activity by Engineered Mutations
- (2013) Zhe Zhang et al. PLoS Computational Biology
- All-Atom Structural Investigation of Kinesin–Microtubule Complex Constrained by High-Quality Cryo-Electron-Microscopy Maps
- (2012) Minghui Li et al. BIOCHEMISTRY
- Predicting folding free energy changes upon single point mutations
- (2012) Zhe Zhang et al. BIOINFORMATICS
- SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models
- (2012) Iain H. Moal et al. BIOINFORMATICS
- The Continuum Model of Selection in Human Tumors: General Paradigm or Niche Product?
- (2012) S. Leedham et al. CANCER RESEARCH
- Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization
- (2012) Yibing Shan et al. CELL
- Mutational Processes Molding the Genomes of 21 Breast Cancers
- (2012) Serena Nik-Zainal et al. CELL
- An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity
- (2012) Kyoko Takano et al. HUMAN MOLECULAR GENETICS
- Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases
- (2012) Kosuke Hashimoto et al. HUMAN MUTATION
- Predicting the Functional Effect of Amino Acid Substitutions and Indels
- (2012) Yongwook Choi et al. PLoS One
- The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.
- (2012) Ethan Cerami et al. Cancer Discovery
- Probing the Structural and Energetic Basis of Kinesin–Microtubule Binding Using Computational Alanine-Scanning Mutagenesis
- (2011) Minghui Li et al. BIOCHEMISTRY
- Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site
- (2011) Gilad Wainreb et al. BIOINFORMATICS
- Protein localization in disease and therapy
- (2011) M.-C. Hung et al. JOURNAL OF CELL SCIENCE
- The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors
- (2011) Henning Stehr et al. Molecular Cancer
- Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation
- (2011) Paul B. Chapman et al. NEW ENGLAND JOURNAL OF MEDICINE
- IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
- (2011) B. A. Shoemaker et al. NUCLEIC ACIDS RESEARCH
- Predicting the functional impact of protein mutations: application to cancer genomics
- (2011) Boris Reva et al. NUCLEIC ACIDS RESEARCH
- In Silico and In Vitro Investigations of the Mutability of Disease-Causing Missense Mutation Sites in Spermine Synthase
- (2011) Zhe Zhang et al. PLoS One
- A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics
- (2011) Shawn Witham et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants
- (2011) Özlem Demir et al. PLoS Computational Biology
- Identification of amino acid residues responsible for increased thermostability of feruloyl esterase A from Aspergillus niger using the PoPMuSiC algorithm
- (2010) Shuai-Bing Zhang et al. BIORESOURCE TECHNOLOGY
- Cbl and Human Myeloid Neoplasms: The Cbl Oncogene Comes of Age: Figure 1.
- (2010) Stephen C. Kales et al. CANCER RESEARCH
- Reaching biological timescales with all-atom molecular dynamics simulations
- (2010) Matthew C Zwier et al. CURRENT OPINION IN PHARMACOLOGY
- Molecular dynamics simulations of protein dynamics and their relevance to drug discovery
- (2010) Freddie R Salsbury Jr CURRENT OPINION IN PHARMACOLOGY
- CanProVar: a human cancer proteome variation database
- (2010) Jing Li et al. HUMAN MUTATION
- Computational analysis of missense mutations causing Snyder-Robinson syndrome
- (2010) Zhe Zhang et al. HUMAN MUTATION
- Performance of protein stability predictors
- (2010) Sofia Khan et al. HUMAN MUTATION
- Molecular dynamics studies of the 3D structure and planar ligand binding of a quadruplex dimer
- (2010) Ming-Hui Li et al. JOURNAL OF MOLECULAR MODELING
- Molecular Dynamics Study on the Interactions of Porphyrin with Two Antiparallel Human Telomeric Quadruplexes
- (2010) Ming-Hui Li et al. JOURNAL OF PHYSICAL CHEMISTRY B
- International network of cancer genome projects
- (2010) Thomas J. Hudson (Chairperson) et al. NATURE
- DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions
- (2010) Dennis M. Kr�ger et al. NUCLEIC ACIDS RESEARCH
- COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
- (2010) S. A. Forbes et al. NUCLEIC ACIDS RESEARCH
- AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements
- (2010) M. Masso et al. PROTEIN ENGINEERING DESIGN & SELECTION
- Modeling Effects of Human Single Nucleotide Polymorphisms on Protein-Protein Interactions
- (2009) Shaolei Teng et al. BIOPHYSICAL JOURNAL
- Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations
- (2009) H. Carter et al. CANCER RESEARCH
- The 3D structures of G-Quadruplexes of HIV-1 integrase inhibitors: molecular dynamics simulations in aqueous solution and in the gas phase
- (2009) Ming-Hui Li et al. JOURNAL OF MOLECULAR MODELING
- Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details
- (2009) V. Potapov et al. PROTEIN ENGINEERING DESIGN & SELECTION
- A three-state prediction of single point mutations on protein stability changes
- (2008) Emidio Capriotti et al. BMC BIOINFORMATICS
- K-rasMutations and Benefit from Cetuximab in Advanced Colorectal Cancer
- (2008) Christos S. Karapetis et al. NEW ENGLAND JOURNAL OF MEDICINE
- Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses
- (2008) S. Jones et al. SCIENCE
- An Integrated Genomic Analysis of Human Glioblastoma Multiforme
- (2008) D. W. Parsons et al. SCIENCE
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