This directory gives data files carefully cross-referencing three well-known functional classification systems to structures in scop (version 1.39). The functional classification schemes are: JUL - Augmented Flybase+ENZYME RILEY - GenProtEC functional classification for E coli MIPS - MIPS scheme for yeast (References for all these schemes as well as scop are given in the PartsList paper, referred to at the bottom. URLs for current versions of everything are given on PartsList.org . The files in this directory are only a partial view of functional classifications as they relate to structure. Users should go to home sites of the functional classifications to get the full classifications.) ############################# 1) Functional Classifications ############################# Here are the raw functional classifications in standardized format. Each file has a slightly different format. riley_cat_decode.txt ~~~~~~~~~~~~~~~~~~~~ 1.5.14 FNT family 1 Cell processes 1.5 Transport/binding protei 1.5.15 FeoB family 1 Cell processes 1.5 Transport/binding protei 1.5.16 GPH family 1 Cell processes 1.5 Transport/binding protei 1.5.17 General PTS family 1 Cell processes 1.5 Transport/bindin 1.5.18 GltS family 1 Cell processes 1.5 Transport/binding protei 111111 222222222222222... Field 1 is function ID number Remaining fields give some definition of function jullookup.txt ~~~~~~~~~~~~~ D 1.2.9.5.1.1.1 Function Primitive: Metabolism | Process: Nucleotides a D 1.3.1.2 Function Primitive: Metabolism | Process: Protein Metabolism an D 1.3.2.4.1.6 Function Primitive: Metabolism | Process: Protein Metabo E 4.6.1.10 Class: Lyases | Subclass: Phosphorus-oxygen lyases | Sub-subclass: N E 4.6.1.5 Class: Lyases | Subclass: Phosphorus-oxygen lyases | Sub-subclass: No E 4.99.1.1 Class: Lyases | Subclass: Other lyases | Sub-subclass: None | Enzyme E 5.1.1.1 Class: Isomerases | Subclass: Racemases and epimerases | Sub-subclass J hormone_relaxin Hormone Relaxin J ion_chann_toxin Toxin that blocks ion channels J lipid_transp Protein that participates in lipid transport J neuro_musc_joint_toxin Toxin that blocks the excitation of muscles by b 1 222222222222222222222222222 33333333333333333333333......... Field 1 is functional classification (D=flybase, E=Enzyme, J=custom) Field 2 is function ID number Remaining fields give some definition of function mips_cat_decode.txt ~~~~~~~~~~~~~~~~~~~ 01 METABOLISM 01.01 amino-acid metabolism 01.01.01 amino-acid biosynthesis 01.01.04 regulation of amino-acid metabolism 01.01.07 amino-acid transport 01.01.10 amino-acid degradation 11111111 2222222222222222222222222222222....... Field 1 is function ID number, either class or subclass Remaining fields give some definition of function ######################################## (2) Relating Functions to Select PDB IDs ######################################## mips_scop_relate.txt riley_scop_relate.txt prejullookup.txt + jullookup.txt These three files relate the functional categories in section 1 to SCOP IDs that have close matches to functionally classified proteins. ##################################### (3) Relating Functions to All PDB IDs ##################################### pdb100id_to_julpdb.dat pdb100id_to_mipspdb.dat pdb100id_to_rileypdb.dat These three files relate ALL the known scop IDs (15198) to the scop IDs that have been classified in section #2. d1a72_1 d3btoa1 99.6 d1deha1 d1deha1 100 d1dehb1 d1deha1 100 d1htba1 d1deha1 99.6 d1htbb1 d1deha1 99.6 d1hdxa1 d1deha1 100 d1hdxb1 d1deha1 100 d1sra__ d1cpn__ 32.3 d1bmoa1 d1cpn__ 32.3 d1bmob1 d1cpn__ 32.3 d1rro__ d3ctn__ 36.9 1111111 2222222 3333 Field 1 is one of all possible scop IDs. Field 2 is a scop ID that has been functionally classified. Field 3 is the precent identity of the match. (Note that an identity less than, say, 90% means that one should NOT use the functional assignment. ) ############## (4) search.cgi ############## search.txt is the actual script that does the lookup for the web form. It should be renamed search.cgi and given execute permission. ######## CITATION: J Qian et al. (2001) PartsList. Nuc. Acids Res. 29: 1750-64 ########