> Tag > Links tagged with 'reproducibility of results'

Links tagged with 'reproducibility of results'

RSS Feed Compact View Sort by Links Directory Index
downloadList as XML List as JSON List as TSV List as CSV

Found 93 links

Displaying 15 links

Hide Resources (5)Hide Databases (7)Hide Tools (81)

3D-JuryTool Content

http://meta.bioinfo.pl/submit_wizard.pl [open in a new window]

Share This Link
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.

links directory index: 775
TitlePublication YearGoogle Scholar Citation Count
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure2003115
3D-Jury: a simple approach to improve protein structure predictions2003592
Detection of reliable and unexpected protein fold predictions using 3D-Jury200368
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence homology computer simulation database management systems humans molecular models protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment tertiary protein structure

3D-pssmTool Content

http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html [open in a new window]

Share This Link
Protein > 3-D Structure Prediction

Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.

links directory index: 1748
TitlePublication YearGoogle Scholar Citation Count
Enhanced genome annotation using structural profiles in the program 3D-PSSM20001568
CAFASP-1: critical assessment of fully automated structure prediction methods1999180
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome bacterial proteins computational biology factual databases flavoproteins integrases molecular models molecular sequence data mycoplasma open reading frames protein folding proteins proteome reproducibility of results retroviridae proteins ribonuclease h secondary protein structure sequence alignment solvents structure-activity relationship

AcromineTool Content

http://www.nactem.ac.uk/software/acromine/ [open in a new window]

Share This Link
Literature > Text Mining and Semantics

Acromine is an tool that finds full forms of acronyms that appear in MEDLINE.

This content is being maintained by pthompson.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
Building a high-quality sense inventory for improved abbreviation disambiguation201012
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms automatic acronym expansion bibliographic databases cluster analysis computational biology dictionaries as topic medline natural language processing polymerase chain reaction reproducibility of results statistical models x-ray computed tomography
setsUniversity of Manchester

Acromine DisambiguatorTool Content

http://www.nactem.ac.uk/software/acromine_disambiguation/ [open in a new window]

Share This Link
Literature > Text Mining and Semantics

Given a biomedical text, Acromine Disambiguator correctly predicts expanded full forms of acronoyms appearing in the text. As acronyms appearing in biomedical texts are often ambiguous, such a disambiguation process is important to ensure the correct interpretation of the text.

This content is being maintained by pthompson.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
Building a high-quality sense inventory for improved abbreviation disambiguation201012
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms automatic acronym disambiguation automatic acronym expansion bibliographic databases cluster analysis computational biology dictionaries as topic medline natural language processing polymerase chain reaction reproducibility of results statistical models x-ray computed tomography
setsUniversity of Manchester

AHMIITool Content

http://www.wdcm.org/AHMII/ahmii.html [open in a new window]

Share This Link
Model Organisms > Microbes
Model Organisms > Other Organisms
Model Organisms > Yeast

Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
AHMII: Agent to Help Microbial Information Integration.20030
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbacteria cell line fungi microbiological techniques reproducibility of results systems integration yeasts

Align-mTool Content

http://bioinformatics.vub.ac.be/software/software.html [open in a new window]

Share This Link
Sequence Comparison > Multiple Sequence Alignments

Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks.

links directory index: 81
TitlePublication YearGoogle Scholar Citation Count
Align-m--a new algorithm for multiple alignment of highly divergent sequences200481
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence amino acid sequence homology genetic variation molecular sequence data protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

links directory index: 627
TitlePublication YearGoogle Scholar Citation Count
Tools for comparative protein structure modeling and analysis2003190
Modeller: generation and refinement of homology-based protein structure models2003437
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

ArrayProspectorTool Content

http://string32.embl-heidelberg.de:8080/prophecies_html/prophecies.html [open in a new window]

Share This Link
Expression > Transcript Expression Analysis

ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
ArrayProspector: a web resource of functional associations inferred from microarray expression data200421
NAR Web Server Issue 2004
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms animals gene expression profiling humans oligonucleotide array sequence analysis proteins reproducibility of results

Berkeley Phylogenomics GroupTool Content

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

Share This Link
DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

This content is being maintained by kimmen.

links directory index: 4963
TitlePublication YearGoogle Scholar Citation Count
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis200720
MUSCLE: multiple sequence alignment with high accuracy and high throughput20044855
SATCHMO: sequence alignment and tree construction using hidden Markov models200388
Phylogenetic inference in protein superfamilies: analysis of SH2 domains.19980
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

BINDTranslationDatabase Content

http://download.baderlab.org/BINDTranslation/ [open in a new window]

Share This Link
Expression > Networks
Other Molecules > Databases
Protein > Databases

Biomolecular Interaction Network Database (BIND): a database of curated biomolecular interactions.

This content is being maintained by baderg.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
The Biomolecular Interaction Network Database in PSI-MI 2.520115
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals controlled vocabulary humans protein binding protein databases proteomics rats reproducibility of results
setsUniversity of Toronto

BPROMPTTool Content

http://www.ddg-pharmfac.net/bprompt/BPROMPT/BPROMPT.html [open in a new window]

Share This Link
Protein > 2-D Structure Prediction
Protein > Localization and Targeting

Bayesian PRediction Of Membrane Protein Topology (BPROMPT) uses a Bayesian Belief Network to combine the results of other membrane protein prediction methods for a protein sequence.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
BPROMPT: A consensus server for membrane protein prediction200337
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbayes theorem eukaryotic cells membrane proteins prokaryotic cells protein sequence analysis reproducibility of results secondary protein structure

CAMPDatabase Content

http://bicnirrh.res.in/antimicrobial [open in a new window]

Share This Link
Other Molecules > Databases

Collection of Anti-Microbial Peptides (CAMP) is a free online database that is manually curated and currently holds 3782 antimicrobial sequences. These sequences are divided into experimentally validated (patents and non-patents: 2766) and predicted (1016) datasets based on their reference literature. Information like source organism, activity (MIC values), reference literature, target and non-target organisms of AMPs are captured in the database. Prediction and sequence analysis tools, including BLAST, are integrated in the database.

links directory index: 36
TitlePublication YearGoogle Scholar Citation Count
CAMP: a useful resource for research on antimicrobial peptides201036
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms anti-infective agents antimicrobial cationic peptides bacterial genome computational biology genetic databases humans nucleic acid databases peptides protein databases reproducibility of results

ClusProTool Content

http://cluspro.bu.edu/login.php [open in a new window]

Share This Link
Protein > Molecular Dynamics and Docking

ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.

links directory index: 511
TitlePublication YearGoogle Scholar Citation Count
Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19201033
PIPER: an FFT-based protein docking program with pairwise potentials2006100
ClusPro: an automated docking and discrimination method for the prediction of protein complexes2004247
ClusPro: a fully automated algorithm for protein-protein docking2004131
NAR Web Server Issue 2004
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms antibodies antigens binding sites biological models chemical models cluster analysis computational biology discriminant analysis energy transfer enzyme inhibitors fourier analysis molecular dynamics simulation molecular models monte carlo method protein binding protein conformation protein interaction mapping protein multimerization proteins reproducibility of results sensitivity and specificity static electricity time factors

CNVerTool Content

http://compbio.cs.toronto.edu/cnver/ [open in a new window]

Share This Link
Human Genome > Sequence Polymorphisms
Sequence Comparison > Pairwise Sequence Alignments

CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage.

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
Detecting copy number variation with mated short reads201023
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms base pairing base sequence chromosome breakage chromosome mapping dna copy number variations dna mutational analysis dna shuffling high-throughput nucleotide sequencing humans reproducibility of results
setsUniversity of Toronto

CPCTool Content

http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp [open in a new window]

Share This Link
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
RNA > Functional RNAs

CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.

This content is being maintained by CPC.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine200741
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals computational biology expressed sequence tags genetic code genetic transcription genetic variation genetic vectors messenger rna mice molecular sequence data nucleic acid databases protein biosynthesis proteins reproducibility of results rna

Associated Tag Cloud