> Tag > Links tagged with 'amino acid sequence'

Links tagged with 'amino acid sequence'

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

Found 100 links

Displaying 15 links

Hide Resources (7)Show Databases (29)Hide Tools (93)

(PS)2 Protein Structure Prediction ServerTool Content

http://ps2.life.nctu.edu.tw [open in a new window]

Share This Link
Protein > 3-D Structure Prediction

(PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T-Coffee for template selection and target-template alignment. The final three-dimensional (3D) structure is built using RAMP or MODELLER.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
(PS)2: protein structure prediction server200627
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence consensus sequence molecular models protein conformation protein sequence analysis sequence alignment

3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/ [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > Networks & Interactions, Pathways and Enzymes

3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
3D-partner: a web server to infer interacting partners and binding models200727
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence amino acid sequence homology binding sites gene expression profiling molecular sequence data protein binding protein databases protein interaction mapping protein sequence analysis proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins 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

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

links directory index: 98
TitlePublication YearGoogle Scholar Citation Count
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures20073
Query3d: a new method for high-throughput analysis of functional residues in protein structures200536
A structural study for the optimisation of functional motifs encoded in protein sequences20047
Three-dimensional profiles: a new tool to identify protein surface similarities199852
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 animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

3MotifTool Content

http://motif.stanford.edu/distributions/3motif/ [open in a new window]

Share This Link
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.

This content is being maintained by brutlag.

links directory index: 20
TitlePublication YearGoogle Scholar Citation Count
3MOTIF: visualizing conserved protein sequence motifs in the protein structure database200310
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs200310
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid motifs amino acid sequence amino acids animals conserved sequence database management systems molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment three-dimensional imaging

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

AlphaPredTool Content

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

Share This Link
Protein > 2-D Structure Prediction

The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.

This content is being maintained by raghavagps.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information200439
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalpha-turns amino acid sequence ANN molecular sequence data neural networks (computer) prediction protein databases protein sequence analysis proteins roc curve secondary protein structure sequence alignment sequence-to-structure network statistical models structure-to-structure network

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

Berkeley Drosophila Genome ProjectResource Content

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

Share This Link
Model Organisms > Fly

Good entrez to fly genome resources.

links directory index: 370
TitlePublication YearGoogle Scholar Citation Count
The Drosophila melanogaster genome200375
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes2002147
A Drosophila full-length cDNA resource2002148
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence animals base sequence cell line cluster analysis complementary dna dna sequence analysis drosophila melanogaster expressed sequence tags gene library genetic databases genome insect genes male membrane glycoproteins membrane proteins molecular sequence data rna sequence alignment testis

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

BetatPred2Tool Content

http://www.imtech.res.in/raghava/betatpred2/ [open in a new window]

Share This Link
Protein > 2-D Structure Prediction

The aim of BetaTPred2 server is to predict ß turns in proteins from multiple alignment by using neural network from the given amino acid sequence. For ß turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED.

This content is being maintained by raghavagps.

links directory index: 94
TitlePublication YearGoogle Scholar Citation Count
Prediction of beta-turns in proteins from multiple alignment using neural network200394
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence beta-turns computer simulation factual databases molecular sequence data multiple sequence alignment neural networks (computer) prediction protein secondary protein structure statistical models

BioBayesNetTool Content

http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/ [open in a new window]

Share This Link
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Sequence Features

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.

links directory index: 33
TitlePublication YearGoogle Scholar Citation Count
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data20078
A multiple-feature framework for modelling and predicting transcription factor binding sites200525
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence automated pattern recognition bayes theorem binding sites chemical models computational biology computer simulation dna sequence analysis genetic models molecular models molecular sequence data protein binding protein conformation protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship transcription factors

BTEVALTool Content

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

Share This Link

The aim of BTEVAL server is to evaluate beta turn prediction algorithms on a uniform data set of 426 proteins or subsets of these proteins. It is the new data set in which no two protein chains have more that 25% sequence identity and each chain contains minimum one beta turn.

This content is being maintained by raghavagps.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
BTEVAL: a server for evaluation of beta-turn prediction methods20033
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence beta-turn btpred chou-fasman computational biology computer simulation gorbturn molecular models molecular sequence data prediction protein protein databases proteins secondary protein structure thornton

CE-MCTool Content

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

Share This Link
Protein > 3-D Structure Comparison
Sequence Comparison > Multiple Sequence Alignments

A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.

links directory index: 146
TitlePublication YearGoogle Scholar Citation Count
CE-MC: a multiple protein structure alignment server200481
A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization200165
NAR Web Server Issue 2004
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence amino acid sequence homology aspartic acid endopeptidases factual databases molecular sequence data monte carlo method protein kinases proteins secondary protein structure sequence alignment software design

CHpredictTool Content

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

Share This Link
Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes

The CHpredict server predict two types of interactions: C-H...O and C-H...π interactions. For C-H...O interaction, the server predicts the residues whose backbone Cα atoms are involved in interaction with backbone oxygen atoms and for C-H...π interactions, it predicts the residues whose backbone Cα atoms are involved in interaction with π ring system of side chain aromatic moieties.

This content is being maintained by raghavagps.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Prediction of C alpha-H...O and C alpha-H...pi interactions in proteins using recurrent neural network20063
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms alpha H O amino acid sequence ANN C alpha H pi computer simulation hydrogen bonding hydrogen bonding interactions molecular models molecular sequence data neural networks (computer) protein databases protein sequence analysis proteins secondary protein structure weak interactions

Associated Tag Cloud