University School of Medicine

Extended Search


Congratulations Philipp Fervers for for the successful defense of his doctoral thesis.
Yukie Kashima, welcome to our institute!
"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.
Welcome Reza Halabian, our new PhD student..
"Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer” by Suzuki et al. has bee published by DNA Research.
"Serotyping dengue virus with isothermal amplification and a portable sequencer.” by Yamagishi at al. has been published by Scientific Reports.
"Contribution of Transposable Elements to Human Proteins" by Makalowski, Kischka and Makalowska has been published by eLS.
"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.
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