According to "structure diversity" values between each pair of protein structures, the program calculate a phylogenetic tree using "neighbor join method" (Saitou & Nei Mol.Biol.Evol.4:406-425, 1987) It outputs the tree in PHYLIP format with name "filetree". This tree file can be used to display graphcally by the DRAWGRAM in PHYLIP package or by the NJPLOT program.Example Input (Unix)
# # input: # PDB filename id zone # cat > t.inp << END !dump yes pdb $PDB/1pyd.pdb 1PYD_ScPDC2 a: pdb $PDB/1pox.pdb 1POX_POX a: pdb $PDB/1bfd.pdb 1BFD match rate 0.5 1.0 residue 3 distance 3.8 END maps < t.inpExample Output
======================================================== M A P S Multiple Alignment OF Proteins Structures Version 0.1 Nov-12-1998 ======================================================== Author: Guoguang Lu Karolinska Institute, Stockholm, Sweden E-mail: guoguang@alfa.mbb.ki.se WWW: http://gamma.mbb.ki.se/~guoguang/maps.html --------------------------------------------------------- .... Total 4 will be used for 3d comparison 4 models will be aligned Model 1 Residues 567 Name: 1ZPD_ZmPDC PDB file: zmA_z.pdb 1 Model 2 Residues 537 Name: 1PYD_ScPDC PDB file: 1pyd_z.pdb 568 Model 3 Residues 585 Name: 1POX_POX PDB file: 1poxA_z.pdb 1105 Model 4 Residues 523 Name: 1BFD PDB file: /nfs/scratch/guoguan 1690 Maxinium residue number 585 .... Average fitting residues: 321.0 ------------------------------------- Matrix of fitting residues ------------------------------------- 1ZPD_ZmP1PYD_ScP1POX_POX1BFD 1ZPD_ZmPDC 1PYD_ScPDC 397. 1POX_POX 335. 279. 1BFD 313. 281. 321. ------------------------------------- Sequence identities of aligned residues ------------------------------------- 1ZPD_ZmP1PYD_ScP1POX_POX1BFD 1ZPD_ZmPDC 1PYD_ScPDC 8.1 1POX_POX 12.5 10.0 1BFD 6.4 7.1 3.7 ------------------------------------- Matrix for fitting scores ------------------------------------- 1ZPD_ZmP1PYD_ScP1POX_POX1BFD 1ZPD_ZmPDC 1PYD_ScPDC 0.9 1POX_POX 1.2 1.7 1BFD 1.3 1.7 1.3 New Matrix 1 1 1 1 0.000 0.872 1.224 1.338 0.872 0.000 1.739 1.709 1.224 1.739 0.000 1.294 1.338 1.709 1.294 0.000 .... Total 2212 residues distance 3.800000 minimum number of residues 3 4 models will be aligned Total 2898 equations with 18 parameters Cycle= 1 RMS 1.064 Mean-distance 0.955 with 161 aligned residues 4 models will be aligned Total 3024 equations with 18 parameters Cycle= 2 RMS 1.073 Mean-distance 0.964 with 168 aligned residues 4 models will be aligned Total 3132 equations with 18 parameters Cycle= 3 RMS 1.086 Mean-distance 0.976 with 174 aligned residues 4 models will be aligned Total 3168 equations with 18 parameters Cycle= 4 RMS 1.096 Mean-distance 0.983 with 176 aligned residues 4 models will be aligned Total 3168 equations with 18 parameters Cycle= 5 RMS 1.096 Mean-distance 0.983 with 176 aligned residues Total 18 fragment with 176 residues are equivalent in this set of the structures Fragment 1 length 13 1ZPD_ZmPDC A22 FAVAGDYNLVLLD A35 1PYD_ScPDC A23 FGLPGDFNLSLLD A36 1POX_POX A30 YGIPGGSINSIMD A43 1BFD 21 FGNPGSNELPFLK 34 | Fragment 2 length 17 1ZPD_ZmPDC A43 EQVYCCNELNCGFSAEG A60 1PYD_ScPDC A44 RWAGNANELNAAYAADG A61 1POX_POX A52 HYIQVRHEEVGAMAAAA A69 1BFD 40 RYILALQEACVVGIADG 57 | | Fragment 3 length 14 1ZPD_ZmPDC A67 AAAVVTYSVGALSA A81 1PYD_ScPDC A68 SCIITTFGVGELSA A82 1POX_POX A77 GVCFGSAGPGGTHL A91 1BFD 65 AFINLHSAAGTGNA 79 | Fragment 4 length 3 1ZPD_ZmPDC A86 GAY A89 1PYD_ScPDC A87 GSY A90 1POX_POX A96 DAR A99 1BFD 84 NAW 87 Fragment 5 length 12 1ZPD_ZmPDC A92 LPVILISGAPNN A104 1PYD_ScPDC A93 VGVLHVVGVPSI A105 1POX_POX A102 VPVLALIGQFGT A114 1BFD 90 SPLIVTAGQQTR 102 | Fragment 6 length 8 1ZPD_ZmPDC A131 ITAAAEAI A139 1PYD_ScPDC A132 ISETTAMI A140 1POX_POX A133 VADYNVTA A141 1BFD 122 LVKWSYEP 130 Fragment 7 length 8 1ZPD_ZmPDC A148 IDHVIKTA A156 1PYD_ScPDC A149 IDRCIRTT A157 1POX_POX A150 IDEAIRRA A158 1BFD 139 MSRAIHMA 147 | Fragment 8 length 14 1ZPD_ZmPDC A159 KKPVYLEIACNIAS A173 1PYD_ScPDC A160 QRPVYLGLPANLVD A174 1POX_POX A161 QGVAVVQIPVDLPW A175 1BFD 151 QGPVYLSVPYDDWD 165 Fragment 8 length 14 1ZPD_ZmPDC A159 KKPVYLEIACNIAS A173 1PYD_ScPDC A160 QRPVYLGLPANLVD A174 1POX_POX A161 QGVAVVQIPVDLPW A175 1BFD 151 QGPVYLSVPYDDWD 165 Fragment 9 length 5 1ZPD_ZmPDC A383 TVIAE A388 1PYD_ScPDC A383 VVIAE A388 1POX_POX A389 IYSID A394 1BFD 371 IYLNE 376 Fragment 10 length 3 1ZPD_ZmPDC A407 EYE A410 1PYD_ScPDC A407 ISQ A410 1POX_POX A414 ITS A417 1BFD 396 YFC 399 Fragment 11 length 4 1ZPD_ZmPDC A413 GHIG A417 1PYD_ScPDC A413 GSIG A417 1POX_POX A420 ATMG A424 1BFD 401 GGLG 405 | Fragment 12 length 6 1ZPD_ZmPDC A418 SVPAAF A424 1PYD_ScPDC A418 TTGATL A424 1POX_POX A425 GIPGAI A431 1BFD 406 ALPAAI 412 Fragment 13 length 3 1ZPD_ZmPDC A427 VGA A430 1PYD_ScPDC A427 FAA A430 1POX_POX A434 LNY A437 1BFD 415 LAE 418 Fragment 13 length 3 1ZPD_ZmPDC A427 VGA A430 1PYD_ScPDC A427 FAA A430 1POX_POX A434 LNY A437 1BFD 415 LAE 418 Fragment 14 length 45 1ZPD_ZmPDC A433 RNILMVGDGSFQLTAQEVAQMVRLKLPVIIFLINNYGYTIEVMIH A478 1PYD_ScPDC A437 RVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIH A482 1POX_POX A440 QVFNLAGDGGASMTMQDLVTQVQYHLPVINVVFTNCQYGFIKDEQ A485 1BFD 421 QVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFA 466 ||| | | Fragment 15 length 4 1ZPD_ZmPDC A481 YNNI A485 1PYD_ScPDC A487 YNEI A491 1POX_POX A494 GVEF A498 1BFD 475 GLDV 479 Fragment 16 length 5 1ZPD_ZmPDC A486 NWDYA A491 1PYD_ScPDC A492 GWDHL A497 1POX_POX A499 DIDFS A504 1BFD 480 GIDFR 485 | Fragment 17 length 3 1ZPD_ZmPDC A494 EVF A497 1PYD_ScPDC A500 PTF A503 1POX_POX A507 DGV A510 1BFD 488 KGY 491 Fragment 18 length 9 1ZPD_ZmPDC A532 PTLIECFIG A541 1PYD_ScPDC A533 IRMIEIMLP A542 1POX_POX A537 PVLIDAVIT A546 1BFD 516 PVLIEVSTV | Total 14 residues are identical among all 4 structures Rate of overall identity 0.080 Statistics for residues which share least identity 1ZPD_ZmPDC 93 0.528 1PYD_ScPDC 104 0.591 1POX_POX 74 0.420 1BFD 77 0.438
Distribution of the program
All rights of the program are reserved. No re-distribution is allowed without
permission from the author. If the program contributes to the work in any
publication, the author should be acknowledged by citing a proper
reference.
The program is free for academic users (The current version is also free for
industry users).
So far, executable code for
DEC/Alpha/OSF1,
Linux/Intel,
SGI IRIX5 and
SGI IRIX6.5
Since Nov 24 MET 1998
