ProAnWin - Protein Analyst for Windows
home software sectionState Research Center of Virology and Biotechnology
The program makes the following: input of sequences from several formats (SWISS-PROT, PIR, FASTA, GCG, CLUSTAL) and 3D structure in PDB format; flexible multiple protein sequences alignment and threading sequences into known 3D structure (ClustalV + manual alignment); input of user-defined protein activities, properties or related phenotypes (with possibility to transform activity: log(x), 1/x, etc.); calculation of many characteristics (hydrophobicity, amphipathicity, etc.) of linear and spatial protein sites; fast multiple (up to eight independent factors) linear regression analysis of structure-activity relationships; activity prediction for untested or mutated proteins; data visualization (regression plots, 3D pictures with sites highlighted, multiple alignments); displaying found sites on sequences and 3D structure. The program has two main related windows - with protein sequences and with 3D structure; any site highlighted in sequences is highlighted in 3D structure and vise versa.
ProAnWin aligns complete set of sequences, subset or any selected block, providing thus possibility for iterative alignment that preserve some previously found blocks or those imposed from some biological data (active center, catalytic residues).
The program can be applied to analysis of various protein-related biological data, to prediction of activity (phenotype) of newly sequenced proteins and to simulation of protein-engineering experiments.
Name Sequence (part) Activity* 41 51 61 71 81 Trigramin alpha QCGEGLCCDQCSFIEEGTVCRIARGDDLDDYCNGRSAGCPRNP 130 Albolabrin .............MKK..I..R............I........ 222 Elegantin ..AD.......R.KKKR.I..R....NP..R.T.Q..D....G 136 Flavoridin ..AD.......R.KKKTGI.......FP..R.T.L.ND...WN 100 Batroxastatin ..A........R.KGA.KI..R....NP..R.T.Q..D....R 133 Applagin ..A........L.MK.....-R.....VN.....I........ 50 Kistrin ........E..K.SRA.KI...P...MP..R.T.Q..D...YH 128 Echistatin alpha E.ES.P..RN.L.LK...I.LR.....M......LTCP..... 56 Bitistatin ..NH.E.....K.KKAR.........WN....T.K.SD..W.H 237 Bitan alpha ..NH.E.....R.KKA..........WN....T.K.SD..W.H 108
* - Activity is measured as the concentration of protein (in nM) required to 50% attenuation of platelet-rich plasma aggregation stimulated by adenosine-diphosphate.
2. The set of synthetic peptides with tested antimicrobial activity
Name Activity* Peptide sequence Analog A2 400 GIHYLSHKSFSKFFAGVGKFTNS Analog A1 100 GIHYLSHKSFSKFFAGVQKFTNS Antisense P 60 GIHYLSHKSFSKFFCGVQKFTNS Analog B1 40 GIHYLSHKSFSKFFKGVQKFTNS Analog B2 40 GIHYLSHKSFSKFFKGVGKFTNS Magainin 2 20 GIGKFLHSAKKFGKAFVGEIMNS Analog C1 20 GIHKLSHKSFSKFFKGVQKFTNS Analog C2 20 GIHKLSHKSFSKFFKGVGKFTNS Analog P1 10 AIHNFAHKSFAKFFRAVKKFANA Analog P2 5 AIHNLAHKSLAKLLRAVKKLANA Analog P3 5 GIHNFAHKSFAKFFRAVKKFANS Analog M2 3 KIHKLAHKLLKKLLKAVKKLAKA
* - Minimal inhibitory concentration (in mcg/ml) against E.coli
3. The set of unrelated peptides with tested immunogenicity.
------------------------------------------------- Protein Oncogene Sequence Immuno- region genicity* ------------------------------------------------- 409-425 C-SRC RLIEDNEYTARQGAKFP 4 468-482 C-SRC NREVLDQVERGYRMP 4 499-508 C-SRC WRRDPEERPT 4 001-018 V-KI-RAS MTEYKLVVVGASGVGKSA 5 119-135 V-KI-RAS DLPSRTVDTKQAQELAR 5 161-175 V-KI-RAS REIRQYRLKKISKEE 2 001-018 V-HA-RAS MTEYKLVVVGARGVGKSA 4 001-018 C-HA(EJ)-RAS MTEYKLVVVGAVGVGKSA 3 001-018 C-HA-RAS MTEYKLVVVGAGGVGKSA 5 029-044 V-HA-RAS VDEYDPTIEDSYRKQV 4 091-108 V-HA-RAS EDIHQYREQIKRVKDSDD 4 126-136 V-HA-RAS ESRQAQALARS 4 146-155 V-HA-RAS AKTRQGVEDA 5 160-179 V-HA-RAS VREIRQHKLRKLNPPDESGP 5 011-024 V-MYB PQESSKAGPPSGTT 4 033-047 V-MYB MAFAHNPPAGPLPGA 3 146-162 V-MYB DNTRTSGDNAPVSCLGE 4 168-186 V-MYB PSPPVDHGCLPEESASPAR 4 170-185 V-MYB PPVDHGCLPEESASPA 2 247-260 V-MYB PFHKDQTFTEYRKM 4 247-265 V-MYB PFHKDQTFTEYRKMHGGAV 4 541-555 V-FES RHSTSSSEQEREGGR 4 584-593 V-FES PEVQKPLHEQ 4 782-796 V-FES FLRTEGARLRMKTLL 4 840-846 V-FES SREAADG 0 893-905 V-FES ASPYPNLSNQQTR 3 901-913 V-FES NQQTREFVEKGGR 4 222-234 V-MYC PPTTSSDSEEEQE 0 323-334 V-MYC RTLDSEENDKRR 4 340-350 V-MYC ERQRRNELKLR 4 363-371 V-MYC NNEKAPKVV 1 389-403 V-MYC RLIAEKEQLRRRREQ 4 395-405 V-MYC EQLRRRREQLK 4 400-406 V-MYC RREQLKH 0
* logarithm of antipeptide antibody titers.
4. Phenotype-genotype correlations. Influenza A virus M2 protein from strains sensitive (labeled "sen") and resistant to amantadine or rimantadine ("res").
Strain Sensitivity Sequence (N-terminal part only) PR8-34 res MSLLTEVETPIRNEWGCRCNGSSDPLAIAANIIGILHLILWILDR MON88 res ....................D.................T...... LEN3-83 res ..........................T...........T...... MOS88 res ..........................T...........T...... MON86 res ..........................T...........T...... SVER82 res ..........................T...........T...... WS33 res ....................D.....V.................. LEN85 res ....................D.....VV................. WSN33 res ....................D....FV.................. LEN49 res ....................D.....VV..........T...... LEN6-83 res ....................D...S.VV..S.............. SWONT81 res ....................D.....VA..S.............. SW29-37 res ....................D.....VA..S.............. SWIA30 res ..........T.........D.....VA..S.............. SWWIS61 res ..........T.S.......D.....VA..S.............. SWIA88 res .................K..D.....VAV.S.............. AA60 sen ....................D.....VV..S.............H KOREA68 sen ....................D.....VV..S......F....... BANG79 sen ....................D.....VV..S.............. FW50 sen ....................D.....VV..S.............. MEM88 sen ....................D.....VV..S.............. USSR77 sen .............Q......D.....VV..S.............. PINALB79 sen ..........T..G.E.K.SD.....V...S.............. SWHK82 sen ..........T..G.E.K.SD.....V...S.............. SWNED85 sen ..........T..G....FSD.....V...S.............. FPVR34 sen ..........T..G.E....D.....I...S............N. MLRDNY78 sen ..........T..G.E.K.SD.....V...S.............. TYMN81 sen ..........T..G.E.K.SD.....V...S.............. TYMN80 sen ..........T..G.E.K.SD.....V...S.............. CKVIC85 sen ..........T..G.E.K.SD.....V...S..............
ProAnWin IS USEFUL IN:
ProMSED, Protein Multiple Sequences EDitor for MS Windows 3.x/95 ("a la" Word for Windows style + ClustalV + manual alignment + amino acid coloring + more): EMBL library: ftp://ftp.ebi.ac.uk/pub/software/dos/promsed NSC library: ftp://ftp.bionet.nsc.ru/pub/biology/vector/promsed.dem/promsed$ IUBio archive: ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed1
Please send your comments and your suggestions to Yves Epelboin, epelboin@lmcp.jussieu.fr .