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Automated inference of molecular mechanisms of disease from amino acid substitutions
2009
Bioinformatics
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Over the last decade, a number of computational methods have been developed to predict whether such amino acid substitutions result in an altered phenotype. ...
Single nucleotide substitutions within protein coding regions are of particular importance owing to their potential to give rise to amino acid substitutions that affect protein structure and function which ...
ACKNOWLEDGEMENTS The authors would like to thank Prateek Kumar and Pauline Ng from the J. Craig Venter Institute for their help with the SIFT tool. ...
doi:10.1093/bioinformatics/btp528
pmid:19734154
pmcid:PMC3140805
fatcat:46h4jv4sone2rc3qrl3z4yiq5u
Ethambutol resistance in Mycobacterium tuberculosis: critical role of embB mutations
1997
Antimicrobial Agents and Chemotherapy
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distinct IS6110 fingerprints confirmed the unique association of substitutions in amino acid residue 306 of EmbB with EMB resistance. ...
Sixty-nine percent of epidemiologically unassociated EMB-resistant organisms had an amino acid substitution not found in susceptible strains, and most (89%) replacements occurred at amino acid residue ...
The ongoing support of A. M. Ginsberg is gratefully appreciated. ...
doi:10.1128/aac.41.8.1677
fatcat:543naeyes5hgtll4si32np7s5i
Ethambutol resistance in Mycobacterium tuberculosis: critical role of embB mutations
1997
Antimicrobial Agents and Chemotherapy
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distinct IS6110 fingerprints confirmed the unique association of substitutions in amino acid residue 306 of EmbB with EMB resistance. ...
Sixty-nine percent of epidemiologically unassociated EMB-resistant organisms had an amino acid substitution not found in susceptible strains, and most (89%) replacements occurred at amino acid residue ...
ACKNOWLEDGMENTS The ongoing support of A. M. Ginsberg is gratefully appreciated. ...
pmid:9257740
pmcid:PMC163984
fatcat:bsoazlta4bdejalgrtfctgupxa
Antimicrobial agent resistance in mycobacteria: molecular genetic insights
1995
Clinical Microbiology Reviews
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A majority of fluoroquinolone-resistant M. tuberculosis isolates have amino acid substitutions in a region of the DNA gyrase A subunit homologous to a conserved fluoroquinolone resistance-determining region ...
Mutations in the katG gene resulting in catalase-peroxidase amino acid alterations nad nucleotide substitutions in the presumed regulatory region of the inhA locus are repeatedly associated with isoniazid-resistant ...
The four M. leprae strains each had a Ser3Leu substitution at amino acid residue 425. ...
doi:10.1128/cmr.8.4.496
fatcat:bau4hymemrdrvclwgvcp6ytck4
Antimicrobial agent resistance in mycobacteria: molecular genetic insights
1995
Clinical Microbiology Reviews
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A majority of fluoroquinolone-resistant M. tuberculosis isolates have amino acid substitutions in a region of the DNA gyrase A subunit homologous to a conserved fluoroquinolone resistance-determining region ...
Mutations in the katG gene resulting in catalase-peroxidase amino acid alterations nad nucleotide substitutions in the presumed regulatory region of the inhA locus are repeatedly associated with isoniazid-resistant ...
The four M. leprae strains each had a Ser3Leu substitution at amino acid residue 425. ...
pmid:8665467
pmcid:PMC172873
fatcat:5k4jmykio5e53eg6byqbi5ci7m
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
2004
Briefings in Bioinformatics
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histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. ...
One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from ...
MEGA software project has been supported by research grants from NIH, NSF and Burroughs-Wellcome Fund to S.K. and NIH and NSF to M.N. ...
doi:10.1093/bib/5.2.150
pmid:15260895
fatcat:nmi5opa5zzex5lwfq63q4zciyy
Characterization of group A Streptococcus strains recovered from Mexican children with pharyngitis by automated DNA sequencing of virulence-related genes: unexpectedly large variation in the gene (sic) encoding a complement-inhibiting protein
1997
Journal of Clinical Microbiology
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Sequence variation was studied in several target genes in 54 strains of group A Streptococcus (GAS) cultured from children with pharyngitis in Mexico City. ...
The gene (sic) encoding an extracellular GAS protein that inhibits complement function was unusually variable among isolates with the emm1 family of alleles, with a total of seven variants identified. ...
J.M.M. is an Established Investigator of the American Heart Association. ...
pmid:9399523
pmcid:PMC230151
fatcat:4ehzlyelyncaznaggv4my4w2ni
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
2005
Bioinformatics
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It currently annotates 28 043 validated SNPs that produce amino acid residue substitutions in human proteins from the SwissProt/TrEMBL database. ...
SNPs that result in amino acid residue changes (nsSNPs) are of critical importance in variation between individuals, including disease and drug sensitivity. ...
Table 1 . 1 List of 13 features used to train an SVM to discriminate between monogenic disease-associated amino acid residue substitutions from OMIM and neutral/positive non-synonymous SNPs from dbSNP ...
doi:10.1093/bioinformatics/bti442
pmid:15827081
fatcat:vdfuvxosjjg25eljpouakufypm
Mutations associated with pyrazinamide resistance in pncA of Mycobacterium tuberculosis complex organisms
1997
Antimicrobial Agents and Chemotherapy
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In striking contrast, 72% of the 67 resistant organisms had pncA mutations that altered the primary amino acid sequence of pyrazinamidase. ...
with mutations associated with pyrazinamide resistance in Mycobacterium tuberculosis complex members was characterized in 67 pyrazinamide-resistant and 51 pyrazinamide-susceptible isolates recovered from ...
We are grateful for the ongoing support of A. M. Ginsberg. ...
doi:10.1128/aac.41.3.636
fatcat:z3ayb2mxffbyhpghyliv7kx7qi
Mutations associated with pyrazinamide resistance in pncA of Mycobacterium tuberculosis complex organisms
1997
Antimicrobial Agents and Chemotherapy
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In striking contrast, 72% of the 67 resistant organisms had pncA mutations that altered the primary amino acid sequence of pyrazinamidase. ...
with mutations associated with pyrazinamide resistance in Mycobacterium tuberculosis complex members was characterized in 67 pyrazinamide-resistant and 51 pyrazinamide-susceptible isolates recovered from ...
We are grateful for the ongoing support of A. M. Ginsberg. ...
pmid:9056006
pmcid:PMC163764
fatcat:peltutxyuvcd5je2yfejjyiv4m
Molecular genetic basis of antimicrobial agent resistance inMycobacterium tuberculosis: 1998 update
1998
Tubercle and Lung Disease
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It is reasonable to believe that development of new therapeutics based on knowledge obtained from the study of the molecular mechanisms of resistance will occur. ...
Amino acid changes in the A subunit of deoxyribonucleic acid gyrase cause fluoroquinolone resistance in most organisms. ...
ACKNOWLEDGEMENTS Research in the laboratory of JMM is supported by Public Health Services Grants AI-37004, DA-09238, AI-41168, and AI-33119, and a grant from the Texas Technology Development and Transfer ...
doi:10.1054/tuld.1998.0002
pmid:10645439
fatcat:x6kvp2wxqzb2ddg3mqhwozobwy
Missense Mutations of Human Hsp60: A Computational Analysis to Unveil Their Pathological Significance
2020
Frontiers in Genetics
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inferred from crystal structures. ...
of the amino acids in the human Hsp60 and/or in the highly similar bacterial ortholog GroEL; (c) the location of the mutant amino acids in the monomers and oligomers; and (d) structure-function relationships ...
inferred from crystal structures. ...
doi:10.3389/fgene.2020.00969
pmid:33014020
pmcid:PMC7461820
fatcat:zu64a56tj5bglnersgw6cdodmy
Regulator of G-protein signaling 4 (RGS4)
2010
Science-Business eXchange
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Out of these 44 SNPs, 36% of amino acid substitutions were identified as deleterious by the SIFT program, 42% of amino acid substitutions were identified as damaging by PolyPhen-2 program, 57% and 47% ...
A total of 44 variants were retrieved from dbSNP for the RGS4 gene in Homo sapiens. ...
ACKNOWLEDGEMENTS The authors would like to thank School of Biosciences and Technology, VIT University for providing the facilities to carry out this work and for supporting in its timely completion. ...
doi:10.1038/scibx.2010.521
fatcat:i6z5eqo4ezbbpbmezlcwva4yce
Mutation analysis of CRYAA, CRYGC, and CRYGD associated with autosomal dominant congenital cataract in Brazilian families
2009
Molecular Vision
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Both tyrosine in amino acid 56 in CRYGD and arginine in amino acid 12 in CRYAA have been highly conserved throughout evolution in different species. ...
Congenital cataracts are one of the most treatable causes of visual impairment and blindness during infancy. Approximately 50% of all congenital cataract cases may have a genetic cause. ...
ACKNOWLEDGMENTS We thank all the members of the participating families. This study was supported by CAPES and FAP-SCSP (Santa Casa de São Paulo School of Medicine, São Paulo, Brazil). ...
pmid:19390652
pmcid:PMC2671581
fatcat:mze4imubzzd27k7mlxqbezwjea
Rapid Molecular Genetic Subtyping of Serotype M1 Group A Streptococcus Strains
1999
Emerging Infectious Diseases
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Alignment of inferred N-terminal amino acid sequences of 33 alleles of emm1. The region shown represents amino acids 27 through 110 (GenBank accession number X07860). ...
Moreover, most of the amino acid changes were radical replacements, that is, those producing charge changes or polar-nonpolar substitutions. ...
doi:10.3201/eid0502.990210
pmid:10221878
pmcid:PMC2640708
fatcat:n6qcpmtumzgzxd5uwfaaeob6s4
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