University School of Medicine

Extended Search


"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.
Congrats to Gesche Frohwitter, external candidate, for her successful defense of her thesis :)
Welcome to our institute, Mahsa :)
"Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii" by Jakalski et al. has been published by Biology Direct.
“Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals” by Chernikova et al. has been published by Life.
"TMAinspiration: Decode Interdependencies in Multifactorial Tissue Microarray Data" has been published by Florian B, Horst B, Nikhil V. M and Eberhard K
Welcome to our institute, Victoria and Philipp :)
"Mycophenolic Acid and Its Derivatives as Potential Chemotherapeutic Agents Targeting Inosine Monophosphate Dehydrogenase in Trypanosoma congolense" by Suganuma, Jakalski et al. has been published in Antimicrobial Agents and Chemotherapy.
Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data by Kuritzin, Kischka et al. has been published by PLoS Computational Biology.
"Protein import complexes in the mitochondrial outer membrane of Amoebozoa representatives" by Buczek et al. has been published by BMC Genomics.
"The second European interdisciplinary Ewing sarcoma research summit - A joint effort to deconstructing the multiple layers of a complex disease" by Korsching E and others

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