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2017-07-11
Congratulations Philipp Fervers for for the successful defense of his doctoral thesis.
2017-07-24
Yukie Kashima, welcome to our institute!
2017-07-11
"Inferring clonal structure in HTLV-1-infected individuals: towards bridging the gap between analysis and visualization” by Farmanbar et al. has bee published by Human Genomics.
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2017-07-03
Welcome Reza Halabian, our new PhD student..
2017-06-27
"Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer” by Suzuki et al. has bee published by DNA Research.
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2017-07-14
"Serotyping dengue virus with isothermal amplification and a portable sequencer.” by Yamagishi at al. has been published by Scientific Reports.
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2017-04-21
"Contribution of Transposable Elements to Human Proteins" by Makalowski, Kischka and Makalowska has been published by eLS.
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2017-04-25
"Multicolor immuno- fluorescence reveals that p63- and or K5-positive progenitor cells contribute to normal breast epithelium and usual ductal hyperplasia but not to low-grade intraepithelial neoplasia of the breast." by Boecker / Korsching et al. has been published by Virchows Archiv.
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2017-03-07
Congratulations to Marcin Jakalski for the successful defense of his PhD thesis.

Protein Tools and Browsers

  • SwissTools -- large collection of protein tools and databases
  • Translate -- translates DNA into 6 frames
  • ReverseTrans 1+ 2 -- reverse-translates protein into DNA
  • SAPS -- statistical analysis of protein sequences
  • Emboss -- peptide information and statistics
  • Signalp -- predicts signal peptide cleavage sites
  • Psort -- protein sorting signals
  • TMpred -- predicts transmembrane segments and orientation
  • TMHMM -- predicts transmembrane helices
  • TopPred2 -- topological prediction of membrane proteins
  • TMAP -- predicts membrane proteins from multiple alignment
  • COILS 1+ 2 -- prediction of coiled-coil regions in proteins
  • PREDATOR -- secondary structure from multiple sequences
  • SSCP -- predicts helix, strand and coil from composition
  • STRIDE -- secondary structure from atomic coordinates
  • BCM SS -- secondary structure by four methods
  • Jpred -- consensus method for secondary structure prediction
  • TOPS -- protein topology atlas and tool collection
  • Interpro -- integrated resource of protein families, domains and sites
  • Pfam -- alignments and hidden Markov models of protein domains
  • SMART -- simple modular architecture research tool
  • ProDom -- protein domain database
  • ScanProsite -- scans a sequence against PROSITE
  • ProfileScan -- scans sequence against profile databases
  • FingerPRINTScan -- search tool for Prints motifs
  • ppsearch -- pattern search tool for DNA or protein motifs
  • HMMER -- profile hidden Markov models for sequence analysis
  • SAM -- sequence alignment and modelling system by HMM
  • BLOCKS -- aligns ungapped segments of conserved protein regions
  • IMPALA -- blast search of BLOCKS conserved protein regions
  • Blimps -- improved BLOCKS search tool
  • Motif -- searches for motifs in query sequence
  • FPS -- family pairwise search library of protein families
  • Cognitor -- compare sequence to clusters of orthologous proteins
  • Scop -- structural classification of proteins
  • SuperFamily -- genomewide structural classification of proteins
  • Pratt -- search for conserved patterns in protein sequences
  • Cath -- hierarchical classification of protein domain structures
  • MAST -- motif alignment search tool
  • MEME -- analyzes protein and DNA for motifs
  • Profam -- curated protein classification and homology domains
  • TIGRFAMs -- protein families based on hidden Markov models
  • ProtClass -- protein classification browser
  • Argos -- protein surface and secondary structure tools
  • Dali -- coordinates of query compared to PDB database
  • 123D -- predicts tertiary structure
  • 3Dee -- database of protein domain definitions
  • FSSP -- fold classification based on structure
  • PredProt -- predicts protein structure
  • PredictProt -- threading, secondary, solvent and transmembrane
  • Fold -- 3D structures based on homologous sequences
  • MaxSprout -- protein backbone and side chains from alpha coordinates
  • CE -- finds structural alignments from PDB
  • PQS -- protein quaternary structure query form at EBI
  • DIP -- database of interacting proteins
  • ProtFam -- average core structures for families from structure
  • SCWRL -- sidechain placement using a rotamer library
  • ASC -- analytic surface calculation package
  • AA Contacts -- residue contacts, solvent accessibility
  • ProStar -- protein potential site
  • Sweet -- constructs 3D models of oligosaccharides from formula
  • GlycoSuiteDB -- curated relational database of glycan structures
  • SwissPdbView -- deep view for manipulation and analysis of PDB structures
  • PBD Viewers -- choices of plug-ins and 3D structure viewers
  • Kinemages -- interactive 3D protein web display
  • RasMol -- molecular visualization resource
  • ProtExplorer -- macromolecular viewer related to RasMol
  • Chime -- interactive web plug-in for 3D molecular structures
  • Morph -- downloadable protein shape morpher
  • COMBOSA3D -- combines alignment, protein 3D, and Chime to color
  • Boxshade -- pretty shading of multiple alignments
  • ProtCol -- tool for coloring proteins, default is by hydrophobicity
  • ProtExpl -- protein explorer interactive software