> Tag > Links tagged with 'reproducibility of results'

Links tagged with 'reproducibility of results'

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Found 93 links

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NAPSTool Content

http://proteomics.bioengr.uic.edu/NAPS [open in a new window]

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Protein > Sequence Features

NAPS is a web server for the prediction of specific residues involved in nucleic acid-binding proteins (NAPS) binding to nucleic acid. Amino acid residues involved in DNA and RNA binding are predicted.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
NAPS: a residue-level nucleic acid-binding prediction server20107
NAR Web Server Issue 2010
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tagsalgorithms binding sites dna-binding proteins protein sequence analysis reproducibility of results rna-binding proteins

Netgene2Tool Content

http://www.cbs.dtu.dk/services/NetGene2/ [open in a new window]

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Expression > Splicing

The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

links directory index: 447
TitlePublication YearGoogle Scholar Citation Count
Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information1996447
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tagsalgorithms arabidopsis artificial intelligence exons expert systems factual databases forecasting genetic models green fluorescent proteins introns luminescent proteins molecular sequence data neural networks (computer) plant dna plant rna reproducibility of results rna precursors rna splicing

NetOGlyc Prediction ServerTool Content

http://www.cbs.dtu.dk/services/NetOGlyc/ [open in a new window]

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Other Molecules > Carbohydrates
Protein > Domains and Motifs

Predicts mucin type GalNAc O-glycosylation sites in mammalian proteins.

links directory index: 771
TitlePublication YearGoogle Scholar Citation Count
NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility1998413
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins1997119
Prediction of O-glycosylation of mammalian proteins: specificity patterns of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase1995239
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tagsalgorithms amino acid sequence animals binding sites carbohydrate conformation factual databases glycoproteins glycosylation hiv envelope protein gp120 humans information systems mammals membrane glycoproteins molecular sequence data mucins n-acetylgalactosaminyltransferases n-acetylglucosaminyltransferases neural networks (computer) protein conformation reproducibility of results secondary protein structure serine substrate specificity threonine viral envelope proteins

NetPhosTool Content

http://www.cbs.dtu.dk/services/NetPhos/ [open in a new window]

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Protein > Sequence Features

NetPhos is a neural network-based method for predicting potential phosphorylation sites at serine, threonine or tyrosine residues in protein sequences

links directory index: 1539
TitlePublication YearGoogle Scholar Citation Count
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites19991539
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tagsamino acid motifs amino acid sequence animals binding sites consensus sequence eukaryotic cells glycosylation molecular models neural networks (computer) nuclear proteins phosphoproteins phosphorylation phylogeny reproducibility of results sensitivity and specificity serine substrate specificity tertiary protein structure threonine trans-activators tyrosine

NQ-FlipperTool Content

https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.php [open in a new window]

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Protein > 3-D Structure Prediction

NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.

links directory index: 55
TitlePublication YearGoogle Scholar Citation Count
NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures200718
Self-consistent assignment of asparagine and glutamine amide rotamers in protein crystal structures200618
NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures200619
NAR Web Server Issue 2007
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tagsamides asparagine computational biology crystallography escherichia coli glutamine molecular conformation molecular models protein conformation protein databases protein folding proteins reproducibility of results statistical data interpretation stereoisomerism structural models thermodynamics

OligoWizTool Content

http://www.cbs.dtu.dk/services/OligoWiz2/ [open in a new window]

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DNA > Tools For the Bench
Expression > Transcript Expression Analysis

OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.

links directory index: 175
TitlePublication YearGoogle Scholar Citation Count
OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes200565
Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays2003110
NAR Web Server Issue 2005NAR Web Server Issue 2003
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tagsalgorithms dna primers gene expression profiling genetic transcription molecular sequence data nucleic acid conformation nucleic acid denaturation oligonucleotide array sequence analysis oligonucleotide probes reproducibility of results rna sequence analysis saccharomyces cerevisiae systems integration temperature

PEP-FOLDTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD [open in a new window]

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Protein > 3-D Structure Prediction

PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphide bonded cyclic peptides with 9-36 amino acids using benchmarked peptides.

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links directory index: 43
TitlePublication YearGoogle Scholar Citation Count
PEP-FOLD: an online resource for de novo peptide structure prediction200943
NAR Web Server Issue 2009NAR Web Server Issue 2012
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tagsalgorithms internet molecular models peptides protein conformation protein sequence analysis reproducibility of results software user-computer interface

PfoldTool Content

http://www.daimi.au.dk/~compbio/pfold [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.

links directory index: 560
TitlePublication YearGoogle Scholar Citation Count
Pfold: RNA secondary structure prediction using stochastic context-free grammars2003280
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history1999280
NAR Web Server Issue 2003
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tagsalgorithms bacterial rna base sequence biological evolution catalytic rna computational biology computer simulation endoribonucleases molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology probability reproducibility of results ribonuclease p rna rna sequence analysis sequence alignment stochastic processes time factors

PHOGTool Content

http://phylofacts.berkeley.edu/orthologs/ [open in a new window]

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Protein > Phylogeny Reconstruction

The PHOG web server identifies orthologs based on precomputed phylogenetic trees in the PhyloFacts resource. Users may target different taxonomic distances and precision levels by using tree-distance thresholds.

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links directory index: 29
TitlePublication YearGoogle Scholar Citation Count
Berkeley PHOG: PhyloFacts orthology group prediction web server200929
NAR Web Server Issue 2009
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tagsalgorithms animals humans mice phylogeny protein sequence analysis reproducibility of results

PI2PETool Content

http://pipe.scs.fsu.edu/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes

PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.

links directory index: 473
TitlePublication YearGoogle Scholar Citation Count
PI2PE: protein interface/interior prediction engine200718
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces200751
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence200549
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data2005111
Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading200136
Prediction of protein interaction sites from sequence profile and residue neighbor list2001208
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids animals artificial intelligence binding sites biomolecular nuclear magnetic resonance computational biology computer simulation dna dna-binding proteins factual databases genomic library hydrophobic and hydrophilic interactions membrane proteins molecular conformation molecular models molecular sequence data mutation mycoplasma neural networks (computer) open reading frames prions protein binding protein conformation protein sequence analysis proteins quaternary protein structure reproducibility of results rna-binding proteins saccharomyces cerevisiae secondary protein structure sequence alignment solvents

PicXAA-WebTool Content

http://gsp.tamu.edu/picxaa/ [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

PicXAA-Web is a web tool for probablistic alignment of multiple biological sequences using probabilistic non-progressive alignment algorithms. Multiple protein, DNA and RNA sequences may be analyzed.

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences.20110
NAR Web Server Issue 2011
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tagsalgorithms dna sequence analysis protein sequence analysis reproducibility of results rna sequence analysis sequence alignment

PipeAlignTool Content

http://bips.u-strasbg.fr/PipeAlign/ [open in a new window]

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Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.

links directory index: 470
TitlePublication YearGoogle Scholar Citation Count
LEON: multiple aLignment Evaluation Of Neighbours200426
PipeAlign: A new toolkit for protein family analysis200385
RASCAL: rapid scanning and correction of multiple sequence alignments200389
Density of points clustering, application to transcriptomic data analysis200232
Secator: a program for inferring protein subfamilies from phylogenetic trees200154
Ballast: blast post-processing based on locally conserved segments200024
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches2000160
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial proteins caenorhabditis elegans cluster analysis computational biology conserved sequence cytoplasmic and nuclear receptors factual databases fungal proteins gene expression profiling genetic transcription genomics haemophilus influenzae humans leukemia molecular sequence data phylogeny predictive value of tests protein databases protein sequence analysis proteins pyrococcus reproducibility of results saccharomyces cerevisiae sensitivity and specificity sequence alignment small nuclear ribonucleoproteins

POBOTool Content

http://ekhidna.biocenter.helsinki.fi/poxo/pobo/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists.

This content is being maintained by mkankain.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
POXO: a web-enabled tool series to discover transcription factor binding sites20067
POBO, transcription factor binding site verification with bootstrapping200430
NAR Web Server Issue 2004
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tagsarabidopsis binding sites computational biology dna sequence analysis gene expression regulation genetic promoter regions reproducibility of results transcription factors transcriptional regulatory elements

PONGOTool Content

http://pongo.biocomp.unibo.it/ [open in a new window]

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

PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins200630
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites200343
NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence automated pattern recognition humans lipoproteins membrane proteins neural networks (computer) protein conformation protein sequence analysis protein sorting signals reproducibility of results sensitivity and specificity sequence alignment

POXOTool Content

http://www.bioinfo.biocenter.helsinki.fi/poxo [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.

This content is being maintained by mkankain.

links directory index: 92
TitlePublication YearGoogle Scholar Citation Count
POXO: a web-enabled tool series to discover transcription factor binding sites20067
POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets200510
Theme discovery from gene lists for identification and viewing of multiple functional groups200545
POBO, transcription factor binding site verification with bootstrapping200430
NAR Web Server Issue 2006
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tagsarabidopsis binding sites cluster analysis computational biology dna sequence analysis down-regulation gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics hydrogen peroxide itraconazole oligonucleotide array sequence analysis reproducibility of results software design statistical data interpretation transcription factors transcriptional regulatory elements up-regulation

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