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Defining BioInformatics
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This contains information about universities that are offering bioinformatics degree programs.
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Contains information about bioinformatics resources including databases, tools and techniques.
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Home » 2011 » August » 11 » Protein Sequence And Structure Analysis Tools
5:31 PM Protein Sequence And Structure Analysis Tools |
Protein sequence and structure analysis tools
- Physicochemical properties
- ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)
- ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)
- Analyse primary sequence
- ProtColourer (Make colour-coded representation of an amino acid sequence at EBI)
- ProtScale (Hydrophobicity, other conformational parameters, etc. at ExPASy)
- SAPS (Statistical Analysis for charge clusters, repeats, hydrophobic regions, compositional domains etc. at ISREC, CH)
- SignalP (Prediction of peptide signal sequence at CBS, Denmark)
- TargetP (Prediction of subcellular localization at CBS, Denmark)
- PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
- NetOGlyc (Prediction of O-glycosylation sites in mammalian proteins at CBS, Denmark)
- DGPI (Prediction of GPI-anchor and cleavage sites, University of Geneva, CH)
- NetPhos (Prediction of phosphorylation sites in eukaryotic proteins at CBS, Denmark )
- Scansite (Prediction of phosphorylation sites and protein binding sites at MIT, Cambridge, USA)
- Helical Wheel (Representation of alpha-helical peptides)
- Other primary sequence analysis tools at ExPaSy
- Alignment
- Pairwise
- Blast 2 Sequences (Alignment of two protein sequences using BLAST at NCBI, USA)
- SIM (Alignment of 2 protein sequences at ExPASy, Switzerland)
- Pairwise sequence alignment (at Baylor College of Medecine, USA)
- Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
- Multiple
- ClustalW (at EBI, UK)
- ClustalW (at the Baylor College of Medicine, USA)
- MAP (Multiple alignment of (long) sequences without penalizing large gaps)
- Multiple sequence alignment (at Baylor College of Medecine, USA)
- AMAS (Analyze multiple aligned sequences at Oxford University, UK)
- Editors
- CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
- BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)
- Predict secondary structure
- TMpred (Prediction of membrane-spanning regions and their orientation at ISREC).
- TMHMM (Prediction of transmembrane helices in proteins at CBS, Denmark)
- SOSUI (Prediction of Transmembrane Regions, JP)
- PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
- DAS (Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method, Stockholm University)
- HMMTOP (Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences)
- TopPred2 (Topology prediction of membrane proteins at the Institut Pasteur, Paris, France)
- PredictProtein (Protein secondary structure prediction at EMBL)
- JPred (Protein secondary structure prediction at Dundee University, UK)
- HNN (Hierarchical Neural Network secondary structure prediction at NPS@, Lyon, France)
- PSIpred (Protein secondary structure prediction at Brunel University, UK)
- nnPredict (Protein secondary structure prediction at UCSF, CA, USA)
- Other secondary structure prediction tools at ExPASy
- BTPRED (Prediction of beta-turns at UCL, UK)
- Coils (Prediction of coiled Coil regions Lupas' method at EMBnet-CH)
- PairCoil (Prediction of coiled Coil regions by Berger's method)
- MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies at WI, USA)
- TOPS (Protein topology cartoon generation at University of Leeds, UK)
- Analyse and model 3D structure
- 3D viewers
- 3D analysis
- TOPS
(Protein topology cartoon generation at University of Leeds, UK)- DOMPLOT
- (Generate schematic diagrams of the structural domain organisation annotated by ligand contacts at University College London, UK)
- OCA
- (Structure database browser at EBI, UK)
- STRUCTURE
- (Molecular Modeling Database MMDB from ENTREZ at NCBI)
- PsiPred
- (Sequence profile based fold recognition at Brunel University, UK)
- Predicting Protein 3D structure based on homologous sequence search
- (EMBL Heidelberg, Germany)
- 123
- (Fold prediction by aligning (threading) to a (set of) structure(s)
- LOCK
- (Compare 3D structures of query and target proteins (PDB codes) and visualize superposed 3D structures at Stanford University, USA)
- CE
- (3-D protein structure comparison and alignment using the combinatorial extension (CE) method at SDSC, USA)
- DALI
- (Automated Protein Structure Alignment at EBI,UK)
- LIBRA
- (LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading at NIG, Jp)
- VAST
- (Structure-structure similarity search at NCBI, US)
- ASC
- (Analytic Surface Calculation of PDB molecules at IMP, Vienna)
- MolSurfer (Calculate and navigate protein-protein interfaces at EML
- , Germany)
- Protein-Protein Interaction Server (UCL, UK)
- 3D homology modeling
- CPHmodels
(Structure prediction by comparative homology modeling at CBS, Denmark)- Swiss-Model
- (Automated protein homology-modeling server at ExPASy, Switzerland)
- 3DCrunch
- (Browse database of modeled Swiss-Prot proteins at ExPASy, Switzerland)
- FAMS
- (Fully Automated Modeling Service at Kitasato University, JP)
- 3D-Jigsaw
- (Comparative modeling server at Imperial Cancer Research Fund, London, UK )
- SDSC1
- (Protein structure homology modeling server at SDSC, USA)
- Meta PP
- (Collection of structure prediction services at Columbia University, USA)
- List of comparative modeling tools (at the Rockefeller University, NY, USA)
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