> Tag > Links tagged with 'mutation'

Links tagged with 'mutation'

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Found 44 links

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RNAmuteTool Content

http://www.cs.bgu.ac.il/~xrnamute/XRNAmute [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

RNAmute is a web server to facilitate mutational analysis of RNA secondary structures. Single point and multi-point mutations are handled.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
The RNAmute web server for the mutational analysis of RNA secondary structures.20114
NAR Web Server Issue 2011
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tagsmutation nucleic acid conformation rna rna sequence analysis

RosettaDesignTool Content

http://rosettadesign.med.unc.edu [open in a new window]

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Protein > 3-D Structure Prediction
Protein > Biochemical Features

RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.

links directory index: 1600
TitlePublication YearGoogle Scholar Citation Count
RosettaDesign server for protein design200649
Design of a novel globular protein fold with atomic-level accuracy2003716
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins2003170
Accurate computer-based design of a new backbone conformation in the second turn of protein L200263
Computer-based redesign of a protein folding pathway2001158
Conversion of monomeric protein L to an obligate dimer by computational protein design200144
Native protein sequences are close to optimal for their structures2000400
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence amino acid sequence homology bacterial proteins biomolecular nuclear magnetic resonance circular dichroism computational biology computer simulation crystallization dimerization dna-binding proteins guanidine kinetics magnetic resonance spectroscopy molecular models molecular sequence data monte carlo method mutagenesis mutation protein conformation protein databases protein denaturation protein engineering protein folding protein sequence analysis proteins secondary protein structure sequence alignment solubility temperature tertiary protein structure thermodynamics x-ray crystallography

SCMDDatabase Content

http://scmd.gi.k.u-tokyo.ac.jp/ [open in a new window]

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Model Organisms > Yeast

The Sacharomyces Cerevisiae Morphological Database (SCMD) is a collection of micrographs of budding yeast mutants; visualization and data mining tools are provided.

links directory index: 83
TitlePublication YearGoogle Scholar Citation Count
Data mining tools for the Saccharomyces cerevisiae morphological database200513
Development of image processing program for yeast cell morphology200426
SCMD: Saccharomyces cerevisiae Morphological Database200444
NAR Web Server Issue 2005
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tagscell cycle computational biology computer-assisted image processing factual databases fluorescence microscopy genetic databases mutation saccharomyces cerevisiae

SCRATCHTool Content

http://www.igb.uci.edu/servers/psss.html [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Domains and Motifs

SCRATCH is a suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains, beta-residue and beta-strand pairings, amino acid contact maps, and tertiary structure.

links directory index: 295
TitlePublication YearGoogle Scholar Citation Count
SCRATCH: a protein structure and structural feature prediction server2005295
NAR Web Server Issue 2005
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tagsdisulfides mutation protein conformation proteins secondary protein structure solvents tertiary protein structure

SDM Tool Content

http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.php [open in a new window]

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Protein > 3-D Structural Features

Site Directed Mutator (SDM) is a web server for predicting effects of mutations on protein stability and function. Users input a wild type structure and the position and amino acid type of the mutation. An environment specific amino acid substitution frequency for homologous protein families is used to calculate a stability score.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
SDM--a server for predicting effects of mutations on protein stability and malfunction20117
NAR Web Server Issue 2011
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tagsamino acid substitution disease humans mutation protein conformation protein stability proteins thermodynamics

SegemehlTool Content

http://www.bioinf.uni-leipzig.de/Software/segemehl/ [open in a new window]

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DNA > Mapping and Assembly
Sequence Comparison > Other Alignment Tools

segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA).

links directory index: 61
TitlePublication YearGoogle Scholar Citation Count
Fast mapping of short sequences with mismatches, insertions and deletions using index structures200961
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tagsalgorithms base sequence computational biology dna mutational analysis mutation sequence alignment

SelTarbaseDatabase Content

http://www.seltarbase.org [open in a new window]

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Human Genome > Databases

The Selective Targets database is a curated database of a growing number of public mononucleotide repeat tracts (MNR) mutation data in microsatellite unstable human tumors. Regression calculations for various microsatellite instability (MSI) -H tumor entities indicating statistically deviant mutation frequencies predict genes that are shown or highly suspected to be involved in MSI tumorigenesis. Many useful tools for further analyzing genomic DNA, derived wild-type and mutated cDNAs and peptides are integrated. A comprehensive database of all human coding, untranslated, non-coding RNA- and intronic MNRs (MNR_ensembl) is also included.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology201013
NAR Database Issue 2010
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tagsamino acid sequence base sequence computational biology dna repair genetic databases humans immune system microsatellite instability microsatellite repeats molecular sequence data mutation neoplasms nucleic acid databases

SEPACSTool Content

http://fred.bioinf.uni-sb.de/sepacs.html [open in a new window]

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Protein > Annotation and Function

SEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
SePaCS--a web-based application for classification of seroreactivity profiles20074
NAR Web Server Issue 2007
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tagsalgorithms bayes theorem blood proteins brain neoplasms computational biology dna genetic markers glioma humans meningioma mutation neoplastic gene expression regulation oligonucleotide array sequence analysis sensitivity and specificity

SGDDatabase Content

http://www.yeastgenome.org/ [open in a new window]

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Model Organisms > Databases

The Saccharomyces Genome Database (SGD) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae. The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Phenotypes and genetic interaction data are also annotated and displayed in SGD.

This content is being maintained by yeastgenome.

links directory index: 1012
TitlePublication YearGoogle Scholar Citation Count
Saccharomyces Genome Database: the genomics resource of budding yeast20127
Saccharomyces Genome Database provides mutant phenotype data201060
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms2004248
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins200362
Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure199946
SGD: Saccharomyces Genome Database1998589
NAR Database Issue 2010
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tagsamino acid motifs amino acid sequence amino acid sequence homology animals base sequence bibliographic databases computational biology factual databases fungal dna fungal genes fungal genome fungal proteins genetic databases humans information storage and retrieval internet molecular models molecular sequence data molecular weight mutation nucleic acid databases nucleic acid sequence homology phenotype protein conformation protein databases saccharomyces cerevisiae saccharomyces cerevisiae proteins saccharomycetales sequence alignment sequence homology software terminology as topic tertiary protein structure

TGGE-STARTool Content

http://www.charite.de/bioinf/tgge/ [open in a new window]

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DNA > Tools For the Bench

TGGE-STAR assists in the design of PCR primers for temperature gradient gel electrophoresis. It also incorporates the concept of bipolar clamping.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
TGGE-STAR: primer design for melting analysis using PCR gradient gel electrophoresis20023
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tagsdna primers humans microfilament proteins mutation nucleic acid denaturation polyacrylamide gel electrophoresis temperature

TopoGSATool Content

http://www.topogsa.net [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Networks & Interactions, Pathways and Enzymes

TopoGSA (Topology-based Gene Set Analysis) is a web-application dedicated to the computation and visualization of network topological properties for gene and protein sets in molecular interaction networks. Different topological characteristics, such as the centrality of nodes in the network or their tendency to form clusters, can be computed and compared with those of known cellular pathways and processes (Gene Ontology, BioCarta, KEGG, among others). For a detailed description, please refer to the corresponding publication in Bioinformatics (http://bioinformatics.oxfordjournals.org/content/26/9/1271).

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
TopoGSA: network topological gene set analysis201011
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tagsanimals arabidopsis biocarta caenorhabditis elegans computational biology drosophila melanogaster gene gene expression regulation gene ontology gene regulatory networks genetic models humans interpro kegg metacyc mutation neoplasms network analysis pathway analysis protein protein interaction mapping proteins saccharomyces cerevisiae similarity topology

VnDDatabase Content

http://vnd.kobic.re.kr:8080/VnD/ [open in a new window]

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Other Molecules > Databases

The variations and drugs (VnD) is a consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. The VnD database is a useful platform for researchers studying the underlying mechanism for association among genetic variations, diseases and drugs.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
VnD: a structure-centric database of disease-related SNPs and drugs20115
NAR Database Issue 2011
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tagsdisease genetic databases humans mutation pharmaceutical preparations protein conformation proteins single nucleotide polymorphism

WEB-THERMODYNTool Content

http://www.gsa.buffalo.edu/dna/dk/WEBTHERMODYN/ [open in a new window]

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DNA > Structure and Sequence Feature Detection

WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability. This tool can be used to predict sites of low helical stability present at regulatory regions for transcription and replication.

links directory index: 136
TitlePublication YearGoogle Scholar Citation Count
WEB-THERMODYN: Sequence analysis software for profiling DNA helical stability200332
Ease of DNA unwinding is a conserved property of yeast replication origins1993104
NAR Web Server Issue 2003
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tagsdeoxyribonucleases dna dna replication dna sequence analysis fungal chromosomes fungal dna mutation nucleic acid conformation nucleic acid denaturation nucleic acid regulatory sequences plasmids replication origin replicon saccharomyces cerevisiae thermodynamics

Zinc Finger ToolsTool Content

http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.

links directory index: 984
TitlePublication YearGoogle Scholar Citation Count
Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases2006135
Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors2005117
Scanning the human genome with combinatorial transcription factor libraries200394
Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors2001218
Insights into the molecular recognition of the 5'-GNN-3' family of DNA sequences by zinc finger domains2000113
Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences1999307
NAR Web Server Issue 2006
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tagsamino acid sequence animals base sequence binding sites biomolecular nuclear magnetic resonance cell line combinatorial chemistry techniques computer simulation deoxyribonuclease i deoxyribonucleases dna dna primers dna sequence analysis dna-binding proteins down-regulation drug design enzyme-linked immunosorbent assay epidermal growth factor receptor erbb genes erbb-1 genes erbb-2 genes erbb-2 receptor erbb-3 receptor flow cytometry gene expression profiling gene expression regulation gene library gene targeting genetic promoter regions genetic transcription green fluorescent proteins histidine human genome humans kidney luminescent proteins lysine mice molecular cloning molecular models molecular sequence data mutation nucleic acid conformation oligonucleotides peptide library pliability polymerase chain reaction protein conformation protein engineering proteomics recombinant proteins reporter genes retroviridae secondary protein structure sequence analysis site-directed mutagenesis substrate specificity tertiary protein structure transcription factors transfection up-regulation x-ray crystallography zinc fingers

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