> Tag > Links tagged with 'reproducibility of results'

Links tagged with 'reproducibility of results'

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Found 93 links

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GPCRpredTool Content

http://www.imtech.res.in/raghava/gpcrpred/ [open in a new window]

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Protein > Annotation and Function

GPCRpred is a tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence.

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links directory index: 100
TitlePublication YearGoogle Scholar Citation Count
GPCRpred: an SVM-based method for prediction of families and subfamilies of G-protein coupled receptors2004100
NAR Web Server Issue 2004
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tagsartificial intelligence dipeptides g-protein-coupled receptors protein sequence analysis reproducibility of results

HotSpot WizardTool Content

http://loschmidt.chemi.muni.cz/hotspotwizard/ [open in a new window]

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Protein > Annotation and Function
Protein > Biochemical Features
Protein > Sequence Comparison
Protein > Sequence Features

HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
HotSpot Wizard: a web server for identification of hot spots in protein engineering200915
NAR Web Server Issue 2009
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tagsbeta-lactamases glycoside hydrolases hydrolases phosphoric triester hydrolases protein engineering reproducibility of results

Institute of Enzymology ServersTool Content

http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=... [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting

A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.

links directory index: 2004
TitlePublication YearGoogle Scholar Citation Count
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates200546
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content2005392
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins2005235
BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes200552
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank2005138
Transmembrane proteins in the Protein Data Bank: identification and classification2004138
Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation200443
SCide: identification of stabilization centers in proteins.20030
Servers for sequence-structure relationship analysis and prediction20035
On filtering false positive transmembrane protein predictions200257
The HMMTOP transmembrane topology prediction server.20010
Principles governing amino acid composition of integral membrane proteins: application to topology prediction1998795
Stabilization centers in proteins: identification, characterization and predictions1997103
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acids binding sites capsid proteins cell line chemical models computational biology computer simulation conserved sequence cysteine database management systems dna methylation dna primers drug stability energy transfer genome genomics humans hydrophobic and hydrophilic interactions kringles lipid bilayers markov chains membrane proteins molecular models molecular sequence data neural networks (computer) oxidation-reduction pliability polymerase chain reaction protein binding protein conformation protein databases protein engineering protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment statistical models structure-activity relationship sulfites temperature tertiary protein structure thermodynamics tissue plasminogen activator

JVirGelTool Content

http://www.jvirgel.de/ [open in a new window]

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Expression > Protein Expression
Model Organisms > Microbes
Protein > Protein Expression
Protein > Proteomics

JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.

links directory index: 47
TitlePublication YearGoogle Scholar Citation Count
JVirGel: Calculation of virtual two-dimensional protein gels200347
NAR Web Server Issue 2003
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tagscomputer simulation gel electrophoresis isoelectric point molecular weight proteins proteomics reproducibility of results

Kalign, Kalignvu, and MumsaTool Content

http://msa.cgb.ki.se/cgi-bin/msa.cgi [open in a new window]

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Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. Kalignvu is an xml based alignment viewer that allows users to resize alignments and choose different colour schemes. Mumsa is a tool for automatic assessment of alignment quality.

links directory index: 319
TitlePublication YearGoogle Scholar Citation Count
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment200653
Kalign--an accurate and fast multiple sequence alignment algorithm2005198
Automatic assessment of alignment quality200568
NAR Web Server Issue 2006
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tagsalgorithms dna sequence analysis genome genomics nucleic acid databases protein databases protein sequence analysis reproducibility of results roc curve sequence alignment

Loc3DDatabase Content

http://cubic.bioc.columbia.edu/db/LOC3d/ [open in a new window]

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Protein > Localization and Targeting

LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.

links directory index: 343
TitlePublication YearGoogle Scholar Citation Count
Mimicking cellular sorting improves prediction of subcellular localization2005234
Better prediction of sub-cellular localization by combining evolutionary and structural information200376
LOC3D: annotate sub-cellular localization for protein structures200333
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology amino acids animals chloroplasts computational biology computer simulation eukaryotic cells humans neural networks (computer) nuclear localization signals plant proteins protein conformation protein databases protein sequence analysis protein transport proteins proteome reproducibility of results secondary protein structure sequence alignment subcellular fractions

LocalizomeTool Content

http://localodom.kobic.re.kr/LocaloDom/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information200626
NAR Web Server Issue 2006
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tagscell compartmentation eukaryotic cells membrane proteins protein databases reproducibility of results secondary protein structure tertiary protein structure

MaXIC-QTool Content

http://ms.iis.sinica.edu.tw/MaXIC-Q [open in a new window]

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Protein > Proteomics

The MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS20093
NAR Web Server Issue 2009
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tagscomputational biology endothelial cells isotope labeling liquid chromatography mass spectrometry nitric acid peptides proteins reproducibility of results statistical data interpretation

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html [open in a new window]

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The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

links directory index: 3841
TitlePublication YearGoogle Scholar Citation Count
MEME SUITE: tools for motif discovery and searching2009174
MEME: discovering and analyzing DNA and protein sequence motifs2006507
Meta-MEME: motif-based hidden Markov models of protein families1997223
An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases199757
The megaprior heuristic for discovering protein sequence patterns199628
ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool199697
The value of prior knowledge in discovering motifs with MEME1995492
Fitting a mixture model by expectation maximization to discover motifs in biopolymers19942263
NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation base sequence binding sites biopolymers computer communication networks databases as topic dna dna sequence analysis evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases internet mammals markov chains molecular models molecular sequence data nucleic acid repetitive sequences protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements user-computer interface

mGene.webTool Content

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

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DNA > Gene Prediction
Human Genome > Genomics
Model Organisms > General Resources

mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
mGene: accurate SVM-based gene finding with an application to nematode genomes200927
mGene.web: a web service for accurate computational gene finding20098
NAR Web Server Issue 2009
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tagsalgorithms animals artificial intelligence caenorhabditis caenorhabditis elegans computational biology dna sequence analysis genes genomics helminth genes helminth genome proteins reproducibility of results reverse transcriptase polymerase chain reaction rna splice sites transcription initiation site

MICheckTool Content

http://www.genoscope.cns.fr/agc/tools/micheck/ [open in a new window]

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DNA > Annotations

MICheck (Microbial Genome Checker) allows the user to verify gene annotations in previously published microbial genomes.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes200515
NAR Web Server Issue 2005
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tagsbacterial genes bacterial genome genomics nucleic acid databases reproducibility of results time factors

miRTarBaseDatabase Content

http://miRTarBase.mbc.nctu.edu.tw/ [open in a new window]

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RNA > Databases

miRTarBase database contains miRNA-target interactions (MTIs). The collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
miRTarBase: a database curates experimentally validated microRNA-target interactions201135
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsgene expression regulation messenger rna micrornas nucleic acid databases reproducibility of results rna interference systems integration

MITOPREDTool Content

http://bioinformatics.albany.edu/~mitopred/ [open in a new window]

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Protein > Annotation and Function

MITOPRED uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss-Prot and TrEMBL. Users may directly enter or upload a file with a list of protein sequences or Swiss-Prot/TrEMBL accession numbers.

links directory index: 161
TitlePublication YearGoogle Scholar Citation Count
MITOPRED: a web server for the prediction of mitochondrial proteins200451
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins2004110
NAR Web Server Issue 2004
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tagsalgorithms animals cell nucleus gene expression profiling genome humans mitochondrial proteins protein databases protein sequence analysis proteome reproducibility of results sensitivity and specificity sequence alignment software design tertiary protein structure tissue distribution

MolProbityTool Content

http://molprobity.biochem.duke.edu/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
RNA > Structure Prediction, Visualization, and Design

MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts.

This content is being maintained by dcrjsr.

links directory index: 2881
TitlePublication YearGoogle Scholar Citation Count
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids20071156
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes2004401
Structure validation by Calpha geometry: phi,psi and Cbeta deviation20031324
NAR Web Server Issue 2004NAR Web Server Issue 2007
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tagscomputational biology hydrogen bonding hydrogens molecular graphics molecular models molecular structure nucleic acid conformation protein protein conformation reproducibility of results rna structure validation three-dimensional imaging

Mouse Proteome ProjectDatabase Content

http://tap.med.utoronto.ca/mts/ [open in a new window]

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Model Organisms > Mouse and Rat
Protein > Proteomics

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal.

links directory index: 258
TitlePublication YearGoogle Scholar Citation Count
Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling2006258
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tagsanimals cell nucleus computational biology gene expression profiling gene expression regulation genetic transcription green fluorescent proteins messenger rna mice microsomes mitochondria organ specificity organelles protein transport proteins proteomics reproducibility of results
setsUniversity of Toronto

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