SNPeffect
Names
More detailed information about this field from each metasource.
SNPeffect
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
snpeffect
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
Names
More detailed information about this field from each metasource.
SNPeffect
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
snpeffect
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:43.224878
Names
More detailed information about this field from each metasource.
SNPeffect
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
snpeffect
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:43.224878
SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. Further, SNPeffect holds per-variant annotations on functional sites, structural features and post-translational modification.
Description
More detailed information about this field from each metasource.
SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. Further, SNPeffect holds per-variant annotations on functional sites, structural features and post-translational modification.
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
SNPeffect uses computational tools to analyse the effect of coding, non-synonymous SNPs on 3 categories of functional and physico-chemical properties of the affected proteins: - Protein Structure and Dynamics: protein stability (FOLDX), beta-aggregation (TANGO) and amyloidosis (AmyScan). - Integrity of Functional Sites: Catalytic (CSA) and binding sites (Hsp70, ELM). - Cellular Processing: subcellular localisation (PA subcellular), turnover rate (N-terminal rule), post-translational modifcations (O-GlycBase, Phosphobase). Links to the OMIM, PFAM, PDB and SWISSPROT are provided where available.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
This database uses sequence- and structure-based bioinformatics tools to predict the effect of protein-coding SNVs on the structural phenotype of proteins.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:43.224878
Webpage:
http://snpeffect.switchlab.orgWebpage
More detailed information about this field from each metasource.
http://snpeffect.switchlab.org
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://snpeffect.switchlab.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:43.224878
Publications:
Publications
More detailed information about this field from each metasource.
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants
PMID: 22075996
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs
PMID: 15608254
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs
PMID: 16809394
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases
PMID: 18086700
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/GKR996
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants
PMID: 22075996
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs
PMID: 15608254
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs
PMID: 16809394
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases
PMID: 18086700
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/GKR996
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants
PubMed citations: 98.
98 articles citing: SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants
Homozygotes NAT2*5B slow acetylators are highly associated with hepatotoxicity induced by anti-tuberculosis drugs. PMID:35588539
Identification and In Silico Characterization of a Novel COLGALT2 Gene Variant in a Child with Mucosal Rectal Prolapse. PMID:35409030
Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat. PMID:35149708
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. PMID:34953462
Whole-Exome Sequencing Reveals Recurrent but Heterogeneous Mutational Profiles in Sporadic WHO Grade 1 Meningiomas. PMID:34868937
Molecular dynamics and protein frustration analysis of human fused in Sarcoma protein variants in Amyotrophic Lateral Sclerosis type 6: An In Silico approach. PMID:34587215
Somatic Mutation Analysis in Salix suchowensis Reveals Early-Segregated Cell Lineages. PMID:34562099
Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. PMID:34363005
Molecular Dynamics Simulations in Designing DARPins as Phosphorylation-Specific Protein Binders of ERK2. PMID:34361694
Association of Protective HLA-A With HLA-B∗27 Positive Ankylosing Spondylitis. PMID:34335681
Characterization of a RAD51C-silenced high-grade serous ovarian cancer model during development of PARP inhibitor resistance. PMID:34316715
Association of NOS3-c.894G>T transversion with susceptibility to metabolic syndrome in Azar-cohort population: A case-control study and in silico analysis of the SNP molecular effects. PMID:33995953
Understanding the Origins of Loss of Protein Function by Analyzing the Effects of Thousands of Variants on Activity and Abundance. PMID:33779753
Refinement of coding SNPs in the human aryl hydrocarbon receptor gene using ISNPranker: An integrative-SNP ranking web-tool. PMID:33264727
Deciphering the Role of Filamin B Calponin-Homology Domain in Causing the Larsen Syndrome, Boomerang Dysplasia, and Atelosteogenesis Type I Spectrum Disorders via a Computational Approach. PMID:33255942
Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations. PMID:33226070
In silico analysis on the functional and structural impact of Rad50 mutations involved in DNA strand break repair. PMID:32509463
Protein-altering germline mutations implicate novel genes related to lung cancer development. PMID:32393777
Association analysis of rs1695 and rs1138272 variations in GSTP1 gene and breast cancer susceptibility. PMID:32334487
Structure and Aggregation Mechanisms in Amyloids. PMID:32155822
In silico analysis of the tryptophan hydroxylase 2 (TPH2) protein variants related to psychiatric disorders. PMID:32119710
MYC gene associated polymorphisms and Wilms tumor risk in Chinese children: a four-center case-control study. PMID:31700911
CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts. PMID:31296206
VIPdb, a genetic Variant Impact Predictor Database. PMID:31283070
In silico analysis of PFN1 related to amyotrophic lateral sclerosis. PMID:31216283
In silico analysis of the V66M variant of human BDNF in psychiatric disorders: An approach to precision medicine. PMID:30998730
Novel, rare and common pathogenic variants in the CFTR gene screened by high-throughput sequencing technology and predicted by in silico tools. PMID:30996306
Ultra-High-Frequency Reprogramming of Individual Long-Term Hematopoietic Stem Cells Yields Low Somatic Variant Induced Pluripotent Stem Cells. PMID:30840883
Biophysical and Mechanistic Models for Disease-Causing Protein Variants. PMID:30712981
VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants. PMID:30574164
ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis. PMID:30514889
15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms. PMID:30445427
The regulatory role of Toll-like receptors after ischemic stroke: neurosteroids as TLR modulators with the focus on TLR2/4. PMID:30377701
Molecular genetic analysis of weak ABO subgroups in the Chinese population reveals ten novel ABO subgroup alleles. PMID:30201086
The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. PMID:29952048
Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of Rice ERECTA Genes. PMID:29692796
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease. PMID:29590295
Identifying genome-wide immune gene variation underlying infectious disease in wildlife populations - a next generation sequencing approach in the gopher tortoise. PMID:29351737
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. PMID:29254494
Mutation and Suppressor Analysis of the Essential Lipopolysaccharide Transport Protein LptA Reveals Strategies To Overcome Severe Outer Membrane Permeability Defects in Escherichia coli. PMID:29109183
Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes. PMID:28945216
RAC1 Missense Mutations in Developmental Disorders with Diverse Phenotypes. PMID:28886345
Association of C-myc and p53 Gene Expression and Polymorphisms with Hepatitis C (HCV) Chronic Infection, Cirrhosis and Hepatocellular Carcinoma (HCC) Stages in Egypt. PMID:28843220
CD25 expression and outcomes in older patients with acute myelogenous leukemia treated with plerixafor and decitabine. PMID:28718760
Oligomonocytic chronic myelomonocytic leukemia (chronic myelomonocytic leukemia without absolute monocytosis) displays a similar clinicopathologic and mutational profile to classical chronic myelomonocytic leukemia. PMID:28548124
DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins. PMID:28498993
Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses. PMID:28403814
Impact of genetic variation on three dimensional structure and function of proteins. PMID:28296894
Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. PMID:28188128
Mutation-Structure-Function Relationship Based Integrated Strategy Reveals the Potential Impact of Deleterious Missense Mutations in Autophagy Related Proteins on Hepatocellular Carcinoma (HCC): A Comprehensive Informatics Approach. PMID:28085066
Genetic Profiles of Korean Patients With Glucose-6-Phosphate Dehydrogenase Deficiency. PMID:28028996
Dataset of eye disease-related proteins analyzed using the unfolding mutation screen. PMID:27922631
In silico Mapping of Protein Unfolding Mutations for Inherited Disease. PMID:27905547
Angiotensinogen-M235T as a risk factor for myocardial infarction in Asian populations: a genetic association study and a bioinformatics approach. PMID:27586550
G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures. PMID:27565432
The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease. PMID:27564311
The Lack of the Essential LptC Protein in the Trans-Envelope Lipopolysaccharide Transport Machine Is Circumvented by Suppressor Mutations in LptF, an Inner Membrane Component of the Escherichia coli Transporter. PMID:27529623
Protein function in precision medicine: deep understanding with machine learning. PMID:27423136
Amyotrophic Lateral Sclerosis Type 20 - In Silico Analysis and Molecular Dynamics Simulation of hnRNPA1. PMID:27414033
Impacts of Nonsynonymous Single Nucleotide Polymorphisms of Adiponectin Receptor 1 Gene on Corresponding Protein Stability: A Computational Approach. PMID:27294143
Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants. PMID:27171182
Computational approaches for predicting mutant protein stability. PMID:27160393
SPO11-C631T Gene Polymorphism: Association With Male Infertility and an in Silico-Analysis. PMID:27047561
In silico transcriptional regulation and functional analysis of dengue shock syndrome associated SNPs in PLCE1 and MICB genes. PMID:27038471
Late onset variants in Fabry disease: Results in high risk population screenings in Argentina. PMID:26937405
Systematic data-querying of large pediatric biorepository identifies novel Ehlers-Danlos Syndrome variant. PMID:26879370
UMD-Predictor: A High-Throughput Sequencing Compliant System for Pathogenicity Prediction of any Human cDNA Substitution. PMID:26842889
Copy number variation in CEP57L1 predisposes to congenital absence of bilateral ACL and PCL ligaments. PMID:26561035
Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. PMID:26449678
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. PMID:26379229
Increased Aggregation Is More Frequently Associated to Human Disease-Associated Mutations Than to Neutral Polymorphisms. PMID:26340370
Structural modeling and in silico analysis of non-synonymous single nucleotide polymorphisms of human 3β-hydroxysteroid dehydrogenase type 2. PMID:26288759
Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution. PMID:26068475
The road from next-generation sequencing to personalized medicine. PMID:26000024
A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. PMID:25886949
In silico screening, genotyping, molecular dynamics simulation and activity studies of SNPs in pyruvate kinase M2. PMID:25768091
On human disease-causing amino acid variants: statistical study of sequence and structural patterns. PMID:25689729
Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation. PMID:25243403
Single nucleotide variations: biological impact and theoretical interpretation. PMID:25234433
Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics. PMID:24886813
First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. PMID:24723968
Use of long term molecular dynamics simulation in predicting cancer associated SNPs. PMID:24722014
Evolution- and structure-based computational strategy reveals the impact of deleterious missense mutations on MODY 2 (maturity-onset diabetes of the young, type 2). PMID:24578721
AMASS: a database for investigating protein structures. PMID:24497503
Deriving a mutation index of carcinogenicity using protein structure and protein interfaces. PMID:24454733
Structural and functional analysis of human SOD1 in amyotrophic lateral sclerosis. PMID:24312616
MetAmyl: a METa-predictor for AMYLoid proteins. PMID:24260292
Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions. PMID:24124208
Evolutionary reconstruction and population genetics analysis of aurora kinases. PMID:24086628
Association of potentially functional genetic variants of PLCE1 with gallbladder cancer susceptibility in north Indian population. PMID:23975622
Towards precision medicine: advances in computational approaches for the analysis of human variants. PMID:23962656
Molecular mechanisms of disease-causing missense mutations. PMID:23871686
Structural modeling and in silico analysis of human superoxide dismutase 2. PMID:23785434
Candidate gene association studies: a comprehensive guide to useful in silico tools. PMID:23656885
Computational and bioinformatics frameworks for next-generation whole exome and genome sequencing. PMID:23365548
α-Galactosidase aggregation is a determinant of pharmacological chaperone efficacy on Fabry disease mutants. PMID:22773828
FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs. PMID:22684628
Analyzing effects of naturally occurring missense mutations. PMID:22577471 -
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs
PubMed citations: 64.
64 articles citing: SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs
Attacking COVID-19 Progression Using Multi-Drug Therapy for Synergetic Target Engagement. PMID:34071060
Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce. PMID:33846635
Examination of Molecular Effects of MYLK Deletion in a Patient with Extensive Aortic, Carotid, and Abdominal Dissections That Underlie the Genetic Dysfunction. PMID:32655646
Janus Kinase Mutations in Mice Lacking PU.1 and Spi-B Drive B Cell Leukemia through Reactive Oxygen Species-Induced DNA Damage. PMID:32631903
Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation. PMID:32175694
Characterization of a Pathogenic Variant in the ABCD1 Gene Through Protein Molecular Modeling. PMID:32047678
Using mechanistic models for the clinical interpretation of complex genomic variation. PMID:31831811
Campylobacter jejuni isolated from poultry meat in Brazil: in silico analysis and genomic features of two strains with different phenotypes of antimicrobial susceptibility. PMID:31749118
Genomic Observations of a Rare/Pathogenic SMAD3 Variant in Loeys⁻Dietz Syndrome 3 Confirmed by Protein Informatics and Structural Investigations. PMID:31096651
Protein informatics combined with multiple data sources enriches the clinical characterization of novel TRPV4 variant causing an intermediate skeletal dysplasia. PMID:30693671
The regulatory role of Toll-like receptors after ischemic stroke: neurosteroids as TLR modulators with the focus on TLR2/4. PMID:30377701
Personalized molecular modeling for pinpointing associations of protein dysfunction and variants associated with hereditary cancer syndromes. PMID:30043523
Protein molecular modeling techniques investigating novel TAB2 variant R347X causing cardiomyopathy and congenital heart defects in multigenerational family. PMID:29700987
Whole Exome Sequencing and Molecular Modeling of a Missense Variant in TNFAIP3 That Segregates with Disease in a Family with Chronic Urticaria and Angioedema. PMID:29682366
Protein molecular modeling shows residue T599 is critical to wild-type function of POLG and description of a novel variant associated with the SANDO phenotype. PMID:29644085
Genome of Leptospira borgpetersenii strain 4E, a highly virulent isolate obtained from Mus musculus in southern Brazil. PMID:29236926
Leucine to proline substitution by SNP at position 197 in Caspase-9 gene expression leads to neuroblastoma: a bioinformatics analysis. PMID:28324374
Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level. PMID:28302551
Genetic Polymorphism of GABRR2 Modulates Individuals' General Cognitive Ability in Healthy Chinese Han People. PMID:26922432
Association between Genetic Variants in DNA Double-Strand Break Repair Pathways and Risk of Radiation Therapy-Induced Pneumonitis and Esophagitis in Non-Small Cell Lung Cancer. PMID:26901225
Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds. PMID:26865845
Complete Genome Sequences of an Escherichia coli Laboratory Strain and Trimethoprim-Resistant (TMP32XR) Mutant Strains. PMID:26659679
The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome. PMID:26642228
Identifying Highly Penetrant Disease Causal Mutations Using Next Generation Sequencing: Guide to Whole Process. PMID:26106619
Distinctive Genome Reduction Rates Revealed by Genomic Analyses of Two Coxiella-Like Endosymbionts in Ticks. PMID:26025560
Olfactory receptor genes cooperate with protocadherin genes in human extreme obesity. PMID:25943692
Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing. PMID:25909910
Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. PMID:25765346
Complete Genome Sequences of a Mycobacterium smegmatis Laboratory Strain (MC2 155) and Isoniazid-Resistant (4XR1/R2) Mutant Strains. PMID:25657281
Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. PMID:25496777
Single nucleotide variations: biological impact and theoretical interpretation. PMID:25234433
Whole-genome sequence variation, population structure and demographic history of the Dutch population. PMID:24974849
Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs. PMID:24722214
High frequency of rare variants with a moderate-to-high predicted biological effect in protocadherin genes of extremely obese. PMID:24682882
The SAAP pipeline and database: tools to analyze the impact and predict the pathogenicity of mutations. PMID:23819919
Chapter 15: disease gene prioritization. PMID:23633938
Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics approach. PMID:23561625
Gene-expression changes caused by inbreeding protect against inbreeding depression in Drosophila. PMID:22714404
MSV3d: database of human MisSense Variants mapped to 3D protein structure. PMID:22491796
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. PMID:22075996
Linking genotype and phenotype of Saccharomyces cerevisiae strains reveals metabolic engineering targets and leads to triterpene hyper-producers. PMID:21445244
Meet me halfway: when genomics meets structural bioinformatics. PMID:21350909
Improved detection of rare genetic variants for diseases. PMID:21079782
Domain altering SNPs in the human proteome and their impact on signaling pathways. PMID:20886114
CanProVar: a human cancer proteome variation database. PMID:20052754
PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. PMID:19995808
Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. PMID:19289044
SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry. PMID:19036792
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
Distribution and effects of nonsense polymorphisms in human genes. PMID:18852891
SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions. PMID:18315851
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. PMID:18086700
F-SNP: computationally predicted functional SNPs for disease association studies. PMID:17986460
coliSNP database server mapping nsSNPs on protein structures. PMID:17921498
MutDB: update on development of tools for the biochemical analysis of genetic variation. PMID:17827212
Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. PMID:17537826
The SH2B gene is associated with serum leptin and body fat in normal female twins. PMID:17228025
SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences. PMID:16845090
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. PMID:16845085
Fold designability, distribution, and disease. PMID:16680196
Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations. PMID:16595073
SNPs3D: candidate gene and SNP selection for association studies. PMID:16551372
Prediction of water and metal binding sites and their affinities by using the Fold-X force field. PMID:16006526
The FoldX web server: an online force field. PMID:15980494 -
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs
PubMed citations: 40.
40 articles citing: SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs
Ultra-High-Frequency Reprogramming of Individual Long-Term Hematopoietic Stem Cells Yields Low Somatic Variant Induced Pluripotent Stem Cells. PMID:30840883
Implication of OPRM1 A118G Polymorphism in Opioids Addicts in Pakistan: In vitro and In silico Analysis. PMID:30033503
Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch). PMID:29776387
Prediction of a highly deleterious mutation E17K in AKT-1 gene: An in silico approach. PMID:29114575
Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch). PMID:29100531
Leucine to proline substitution by SNP at position 197 in Caspase-9 gene expression leads to neuroblastoma: a bioinformatics analysis. PMID:28324374
Identification of type 2 diabetes subgroups through topological analysis of patient similarity. PMID:26511511
Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution. PMID:26068475
Detection of regulatory SNPs in human genome using ChIP-seq ENCODE data. PMID:24205329
Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics approach. PMID:23561625
Effect prediction of identified SNPs linked to fruit quality and chilling injury in peach [Prunus persica (L.) Batsch]. PMID:23184287
Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. PMID:23181723
Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. PMID:23055974
regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions. PMID:22611130
A novel homozygous p.Arg527Leu LMNA mutation in two unrelated Egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome. PMID:22549407
Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach. PMID:22384055
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. PMID:22075996
Testing rare variants for association with diseases: a Bayesian marker selection approach. PMID:22034989
In silico analysis of single nucleotide polymorphism (SNPs) in human β-globin gene. PMID:22028795
Path to facilitate the prediction of functional amino acid substitutions in red blood cell disorders--a computational approach. PMID:21931771
Complement receptor 1 gene variants are associated with erythrocyte sedimentation rate. PMID:21700265
AnnotQTL: a new tool to gather functional and comparative information on a genomic region. PMID:21596783
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. PMID:21457909
Meet me halfway: when genomics meets structural bioinformatics. PMID:21350909
A knowledge-based weighting framework to boost the power of genome-wide association studies. PMID:21217833
Pharmacogenetics of drug metabolizing enzymes and transporters: effects on pharmacokinetics and pharmacodynamics of anticancer agents. PMID:21194402
Improved detection of rare genetic variants for diseases. PMID:21079782
Computational analysis of missense mutations causing Snyder-Robinson syndrome. PMID:20556796
FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. PMID:20534127
SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. PMID:20529875
Bioinformatic tools for identifying disease gene and SNP candidates. PMID:20238089
PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. PMID:19995808
From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways. PMID:19758470
Association of MICA with rheumatoid arthritis independent of known HLA-DRB1 risk alleles in a family-based and a case control study. PMID:19409079
Next generation tools for the annotation of human SNPs. PMID:19181721
A novel computational and structural analysis of nsSNPs in CFTR gene. PMID:18716917
Applications of computational algorithm tools to identify functional SNPs. PMID:18563462
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. PMID:18086700
A survey of genomic properties for the detection of regulatory polymorphisms. PMID:17559298
PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. PMID:17142238 -
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases
PubMed citations: 28.
28 articles citing: Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases
Multiple genetic factors affecting the pharmacokinetic and pharmacodynamic processes of tacrolimus in Chinese myasthenia gravis patients. PMID:31955224
Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci. PMID:27899403
Lack of Association between NYD-SP18 Variant and Obesity. The Health Alcohol and Psychosocial Factors in Eastern Europe Study. PMID:27237450
Identification of six new susceptibility loci for invasive epithelial ovarian cancer. PMID:25581431
The role of the interactome in the maintenance of deleterious variability in human populations. PMID:25261458
Identification of candidate genes for drought tolerance by whole-genome resequencing in maize. PMID:24684805
Network-based analysis of genome wide association data provides novel candidate genes for lipid and lipoprotein traits. PMID:23882023
Wnt-related genes and large-joint osteoarthritis: association study and replication. PMID:23864140
Polymorphisms in the gene regions of the adaptor complex LAMTOR2/LAMTOR3 and their association with breast cancer risk. PMID:23341997
New advances in the genetic basis of atrial fibrillation. PMID:23066792
In silico profiling of deleterious amino acid substitutions of potential pathological importance in haemophlia A and haemophlia B. PMID:22423892
Bioinformatics for personal genome interpretation. PMID:22247263
Mutation screening of multiple genes in Spanish patients with autosomal recessive retinitis pigmentosa by targeted resequencing. PMID:22164218
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. PMID:22075996
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. PMID:21457909
Targeted genome-wide investigation identifies novel SNPs associated with diabetic nephropathy. PMID:21119753
Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. PMID:21070896
Functional interactions as a survival strategy against abnormal aggregation. PMID:20810784
African signatures of recent positive selection in human FOXI1. PMID:20809947
Bioinformatic tools for identifying disease gene and SNP candidates. PMID:20238089
Common coding variants of the HNF1A gene are associated with multiple cardiovascular risk phenotypes in community-based samples of younger and older European-American adults: the Coronary Artery Risk Development in Young Adults Study and The Cardiovascular Health Study. PMID:20031592
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations. PMID:19758473
Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. PMID:19458495
Association between polymorphisms in RMI1, TOP3A, and BLM and risk of cancer, a case-control study. PMID:19432957
Investigation on the role of nsSNPs in HNPCC genes--a bioinformatics approach. PMID:19389263
Tagging single-nucleotide polymorphisms in candidate oncogenes and susceptibility to ovarian cancer. PMID:19240718
Genetic polymorphisms are associated with serum levels of sex hormone binding globulin in postmenopausal women. PMID:19091090
NYD-SP18 is associated with obesity in the NHLBI Family Heart Study. PMID:18317470 - http://dx.doi.org/10.1093/nar/GKR996
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More detailed information about this field from each metasource.
chaperone binding
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
disease
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
mutation analysis
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
phenotype
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
single nucleotide polymorphism
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
human genes and diseases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
general polymorphism databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
genotype and phenotype
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
structure prediction
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
protein folding, stability and design
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
protein modifications
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:43.224878
Tags
More detailed information about this field from each metasource.
chaperone binding
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
disease
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
gene ontology enrichment
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
mutation analysis
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
phenotype
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
single nucleotide polymorphism
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: SNPeffect; SNPeffect; DOI: https://doi.org/10.25504/FAIRsharing.qbt1gh; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
human genes and diseases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
general polymorphism databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
genotype and phenotype
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:43.224878
proteins
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:43.224878
structure prediction
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:43.224878
protein folding, stability and design
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:43.224878
protein modifications
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:43.224878
chaperone binding disease gene ontology enrichment mutation analysis phenotype single nucleotide polymorphism structure polypeptide region human genes and diseases polymorphism genotype and phenotype proteins structure prediction protein folding, stability and design protein modifications
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