> Tag > Links tagged with 'secondary protein structure'

Links tagged with 'secondary protein structure'

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PfamDatabase Content

http://pfam.sanger.ac.uk/ [open in a new window]

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Protein > Databases

Pfam is a database of protein families and domains. The database uses HMMER3, the latest version of the popular profile hidden Markov model package. Pfam release 24.0 contains 11,912 families.

links directory index: 11859
TitlePublication YearGoogle Scholar Citation Count
The Pfam protein families database.2012212
The Pfam protein families database.20101375
The Pfam protein families database.20081524
Pfam: clans, web tools and services.20061648
The Pfam protein families database.20042639
The Pfam protein families database.20022079
The Pfam protein families database.20001281
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.1999545
Pfam: multiple sequence alignments and HMM-profiles of protein domains.1998556
NAR Database Issue 2010
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tagsalgorithms amino acid sequence amino acid sequence homology animals archaeal genome binding sites caenorhabditis elegans computational biology computer communication networks computer graphics encyclopedias as topic factual databases fungal genome genome genomics humans information storage and retrieval internet macromolecular substances markov chains molecular evolution molecular models molecular sequence data multigene family nucleic acid databases phylogeny protein conformation protein databases protein sequence analysis proteins quality control secondary protein structure sequence alignment software statistics as topic tertiary protein structure user-computer interface

SCOPDatabase Content

http://scop.mrc-lmb.cam.ac.uk/scop/ [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Databases
Protein > Domains and Motifs

Structural Classification of Proteins - database created by a combination of manual inspection and automated methods. Comprehensive ordering of all proteins of known structure, according to evolutionary and structural relationships.

links directory index: 5646
TitlePublication YearGoogle Scholar Citation Count
SCOP database in 2002: refinements accommodate structural genomics2002476
SCOP: a structural classification of proteins database for the investigation of sequences and structures19955170
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tagsalgorithms amino acid sequence amino acid sequence homology animals antibodies capsid proteins computational biology factual databases genome genomics humans information storage and retrieval internet molecular evolution protein conformation protein databases protein folding protein kinases proteins secondary protein structure sequence alignment sequence analysis statistics as topic tertiary protein structure

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

PSORT.orgTool Content

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

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Protein > Localization and Targeting

PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.

links directory index: 3330
TitlePublication YearGoogle Scholar Citation Count
PSORTdb: a protein subcellular localization database for bacteria2005101
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria2003292
Extensive feature detection of N-terminal protein sorting signals2002414
PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization19991544
Better prediction of protein cellular localization sites with the k nearest neighbors classifier1997395
Expert system for predicting protein localization sites in gram-negative bacteria1991584
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence bacterial outer membrane proteins bacterial proteins bayes theorem binding sites cell membrane computational biology cytoplasm decision trees escherichia coli evaluation studies as topic expert systems factual databases fungal proteins gram-negative bacteria humans lipoproteins membrane proteins molecular sequence data neural networks (computer) protein databases protein precursors protein sequence analysis protein sorting signals proteins reproducibility of results saccharomyces cerevisiae secondary protein structure sequence alignment subcellular fractions

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

3D-pssmTool Content

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

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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
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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

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

SOSUI WWW ServerTool Content

http://bp.nuap.nagoya-u.ac.jp/sosui/ [open in a new window]

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Protein > 2-D Structure Prediction

SOSUI is a free online tool that predicts a part of the secondary structure of proteins from a given amino acid sequence (AAS). The main objective is to determine whether the protein in question is a soluble or a transmembrane protein.

links directory index: 1211
TitlePublication YearGoogle Scholar Citation Count
SOSUI: classification and secondary structure prediction system for membrane proteins19981211
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tagsdata display membrane proteins secondary protein structure

Services from Zhou LaboratoryResource Content

http://cssb.biology.gatech.edu/skolnick/people/zhou.html [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Networks & Interactions, Pathways and Enzymes

Tools from the Zhou laboratory including predictors of transmembrane topology (THUMBUP, UMDHMM-TMHP, TUPS); prediction/analysis tools for tertiary structure (SPARKS2, SP3); and, prediction/analysis tools for interactions (DMONOMER, DLOOP, DMUTANT, DCOMPLEX, DDNA, TCD, DOGMA).

links directory index: 1058
TitlePublication YearGoogle Scholar Citation Count
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations200520
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments2005136
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential200473
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition2004135
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding200492
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method200360
Folding rate prediction using total contact distance2002139
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction2002403
NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids antigen-antibody complex binding sites biological evolution chemical models computational biology dimerization factual databases hydrogen bonding kinetics markov chains mathematics membrane proteins molecular evolution molecular structure peptide fragments peptide library plant proteins probability protein binding protein conformation protein databases protein folding protein sequence analysis proteins regression analysis reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical models statistics as topic tertiary protein structure theoretical models thermodynamics time factors

PredictProtein - Sequence Analysis, Structure and Function PredictionResource Content

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

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Protein > 2-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Localization and Targeting
Sequence Comparison > Multiple Sequence Alignments

service for protein structure prediction, protein sequence analysis, protein function prediction, protein sequence alignments, bioinformatics

links directory index: 993
TitlePublication YearGoogle Scholar Citation Count
The PredictProtein server2004776
The PredictProtein server2003217
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tagsartificial intelligence artificial neural network bioinformatics integral membrane proteins multiple sequence alignments neural networks prediction prediction WWW email server protein protein (secondary) structure (solvent accessibility) prediction protein conformation protein databases protein evolution protein sequence analysis protein structure prediction proteins secondary protein structure secondary structure sequence alignment tertiary protein structure time factors transmembrane helices

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

TRAMPLETool Content

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

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

TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.

links directory index: 984
TitlePublication YearGoogle Scholar Citation Count
TRAMPLE: the transmembrane protein labelling environment200510
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins2002160
Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor2001101
HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins199625
Topology prediction for helical transmembrane proteins at 86% accuracy1996688
NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial outer membrane proteins biological models chemical models computer security computer simulation database management systems double-blind method escherichia coli evaluation studies as topic factual databases forecasting haemophilus influenzae humans markov chains membrane proteins molecular models molecular sequence data neural networks (computer) porins protein folding protein sequence analysis protein sorting signals reproducibility of results rhodopseudomonas secondary protein structure sequence alignment software design statistical models

PhobiusTool Content

http://phobius.sbc.su.se/ [open in a new window]

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

Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.

This content is being maintained by lukall.

links directory index: 863
TitlePublication YearGoogle Scholar Citation Count
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server2007176
An HMM posterior decoder for sequence feature prediction that includes homology information2005121
A combined transmembrane topology and signal peptide prediction method2004566
NAR Web Server Issue 2007
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tagsalgorithms artificial intelligence computational biology computer simulation cytoplasm markov chains membrane proteins molecular models probability programming languages protein conformation protein databases protein sorting signals proteomics secondary protein structure statistical models theoretical models

RPBSResource Content

http://bioserv.rpbs.jussieu.fr/ [open in a new window]

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Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Biochemical Features
Protein > Sequence Features

Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).

This content is being maintained by jompo.

links directory index: 852
TitlePublication YearGoogle Scholar Citation Count
RPBS: a web resource for structural bioinformatics200520
Filtering redundancies for sequence similarity search programs20053
Local backbone structure prediction of proteins200443
New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification1999103
PredAcc: prediction of solvent accessibility199945
A global taxonomy of loops in globular proteins199684
Automat and BLAST: comparison of two protein sequence similarity search programs19952
Automat: a novel software system for the systematic search for protein (or DNA) similarities with a notable application to autoimmune diseases and AIDS19948
Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences1987544
NAR Web Server Issue 2005
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tagsacquired immunodeficiency syndrome algorithms amino acid sequence amino acid sequence homology amino acids animals arabidopsis autoimmune diseases azurin bacterial genome chemical models computational biology computer simulation computer-assisted numerical analysis consensus sequence database management systems dna dna sequence analysis evaluation studies as topic factual databases genetic databases globins glycine hiv humans hydrolases leghemoglobin logistic models methods molecular models molecular sequence data nucleic acid sequence homology plant genome plastocyanin protein conformation protein structural homology proteins rats reproducibility of results secondary protein structure sequence alignment sequence analysis sequence homology solvents thiosulfate sulfurtransferase

3D-JuryTool Content

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

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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
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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

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