POM Databases for Macromolecules (version 2, 1998)
Reference: Shindyalov I.N. & Bourne P.E. (1997) Protein data representation and query using optimized data decomposition. CABIOS, 13, 487-496.
Macromolecular Structure
Indices
<![CDATA[
Name Description
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mon Monomer Index]]><![CDATA[
com Compound Index
enc All Entity Index
enp Polymer Entity Index]]><![CDATA[
imm Single Interval Pattern Index
ip6 Multi-interval Pattern Index
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Properties
<![CDATA[
Name Type Size Mem Description
]]><![CDATA[
code3 .mon int1 3 Y Three letter monomer code.
code1 .mon int1 1 Y One letter monomer code.
n_bond .mon int2 1 Y Number of chemical bonds in a monomer.
bond .mon int2 - Y Chemical bonds in monomer.
n_atom .mon int2 1 Y Number of atoms in monomer.
atom .mon int1 - Y Atoms in a monomer.
prev .mon int2 1 Y Atom connected to the previous monomer in the chain.
next .mon int2 1 Y Atom connected to the next monomer in the chain.
type .mon int1 1 Y Monomer type (canonical vs non-canonical).
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id .com int1 4 Y PDB compound ID (if available).
file .com int1 0 Y Source data-file.
status .com int1 1 Y Mask:0x1-no file,0x2-obsolete,0x4-updated.
compnd .com int1 - N Compound name.
source .com int1 - N Source of compound.
date_tex.com int1 - N Deposition date (text).
date_int.com int2 1 Y Deposition date (integer).
header .com int1 - N Functional class of compound.
auth .com int1 - N Author associated with the compound.
jrnl .com int1 - N Primary citation for the compound.
expdta .com int1 1 Y Experimental method.
ec .com int1 - N Enzyme classification code (EC).
res .com flt4 1 Y Resolution of compound.
n_enp .com int2 1 Y Number of polymer entities in the compound.
i_enp .com int4 1 Y Index of first polymer entity in the compound.
n_enc .com int2 1 Y Number of all entities in the compound.
i_enc .com int4 1 Y Index of first entity in the compound.
chi1 .com flt4 1 Y Average standard deviation for all chi1 angles.
fds .com flt4 1 Y Average fds score for whole structure.
obs .com int4 0 Y PDBObs indices of superseding PDB entries.
obs_ids .com int4 0 Y PDB ids of superseding PDB entries.
obs_dat .com int4 1 Y Date of removal from PDB.
reldat .com int4 1 Y Date of release by PDB.
spcgrp .com int1 0 N Space group specification.
spr .com int4 0 Y PDBObs indices of replaced PDB entries.
spr_ids .com int4 0 Y PDB ids of replaced PDB entries.
spr_dat .com int4 1 Y Date of replacement of antecedent version.
unitcell.com int4 6 N Unit cell parameters.
zval .com int4 1 Y Z-Value.
name .enc int1 - Y Entity name.
i_com .enc int4 1 Y Index of compound for the entity.
i_enp .enc int4 1 Y Index of polymer entity for the entity.
n_se .enc int2 1 N Number of subentities in the entity.
se .enc int2 - N Subentities of entity.
sen_pdb .enc int1 - N Subentity numbers for entity (PDB assignment).
n_xyz .enc int4 1 N Number of atoms with coordinates.
xyz .enc flt4 - N Atom coordinates
bfac .enc flt4 - N B factor for atoms.
se_xyz .enc int4 - N Subentity to atoms reference array (i.e., se.enc to xyz.enc).
xyz_se .enc int4 - N Atoms to subentity reference array (i.e., xyz.enc to se.enc).
name .enp int1 - Y Polymer entity name.
i_com .enp int4 1 Y Index of compound for polymer entity.
i_enc .enp int4 1 Y Index of entity for polymer entity.
type .enp int1 1 Y Type (Protein, DNA, RNA).
mw .enp int4 1 Y Polymer entity molecular weight.
n_se .enp int2 1 Y Number of subentities in the polymer entity.
alpha_c .enp flt4 1 Y Alpha helical content of the polymer entity.
beta_c .enp flt4 1 Y Beta structural content of the polymer entity.
alpha_n .enp int2 1 Y Number of alpha helices in the polymer entity.
beta_n .enp int2 1 Y Number of beta structures in the polymer entity.
ss_seg .enp int1 - N Secondary structure by segments in the polymer entity.
seq .enp int1 - Y Sequence of the polymer entity (text).
seq_flt .enp int1 - Y Filtered sequence of the polymer entity (text).
iseq .enp int1 - Y Sequence of the polymer entity (integer).
iseq_flt.enp int1 - Y Filtered sequence of the polymer entity (integer).
c_a .enp flt4 - N C-alpha atoms of the polymer entity.
k_s .enp int1 - Y Secondary structure assignment (Kabsch & Sander, 1983)
exp .enp flt4 - Y Solvent exposure (Lee & Richards, 1971).
exp_flt .enp flt4 - Y Filtered solvent exposure.
pol .enp flt4 - Y Polarity of the local environment.
pol_flt .enp flt4 - Y Filtered polarity of the local environment.
bfac_flt.enp flt4 - Y Filtered B factor of the polymer entity.
se_type .enp int1 - N Subentity type (canonical vs non-canonical).
chi1 .enp flt4 6 N chi1 angle and standard deviation for entity.
fds .enp flt4 1 N fds score for entity.
exp_1b .enp int1 - Y Normalized environment exposure.
pol_1b .enp int1 - Y Normalized environment polarity.
bfac_1b .enp int1 - Y Normalized environment B factor.
sexp_1b .enp int1 - Y Normalized static exposure.
spol_1b .enp int1 - Y Normalized static polarity.
shyd_1b .enp int1 - Y Normalized static hydrophobicity.
svol_1b .enp int1 - Y Normalized static volume.
siso_1b .enp int1 - Y Normalized static isoelectric point.
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Collection Objects
<![CDATA[
Name Type Description
]]><![CDATA[
exp .imm int2 Single interval patterns for env. exposure.
pol .imm int2 Single interval patterns for env. polarity.
bfac .imm int2 Single interval patterns for B factor.
sexp .imm int2 Single interval patterns for static exposure.
spol .imm int2 Single interval patterns for static polarity.
shyd .imm int2 Single interval patterns for static hydrophobicity.
svol .imm int2 Single interval patterns for static volume.
siso .imm int2 Single interval patterns for static isoelectric point.
exp .ip6 int2 Multi-interval patterns for env. exposure.
pol .ip6 int2 Multi-interval patterns for env. polarity.
bfac .ip6 int2 Multi-interval patterns for B factor.
sexp .ip6 int2 Multi-interval patterns for static exposure.
spol .ip6 int2 Multi-interval patterns for static polarity.
shyd .ip6 int2 Multi-interval patterns for static hydrophobicity.
svol .ip6 int2 Multi-interval patterns for static volume.
siso .ip6 int2 Multi-interval patterns for static isoelectric point
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Summary Tables (Property Objects)
<![CDATA[
Name Type Description
exp .pp6 int4 Env. exposure residue propensities (6 val. int.).
pol .pp6 int4 Env. polarity residue propensities (6 val. int.).
bfac .pp6 int4 Env. B factor residue propensities (6 val. int.).
exp .pp8 int4 Env. exposure residue propensities (8 val. int.).
pol .pp8 int4 Env. polarity residue propensities (8 val. int.).
bfac .pp8 int4 Env. B factor residue propensities (8 val. int.).
ks .pp3 int4 Secondary structure residue propensities.
prop8 .ave int4 Environment and static properties residue average.
prop8 .sts flt4 Environment and static properties ranges.
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Protein Structure Alignment
Alignment DB with Feature-Table
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Name Type Size Mem Description
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name .aln_db int1 0 1 Database name
name .aln_fam int1 0 1 Family names
rep .aln_fam int4 1 1 Family representatives
name .aln_enp int1 0 1 Alignment name
fam .aln_enp int4 1 1 Family assignment
fmap5 .aln_enp int4 0 0 Contact map
se_fmap5 .aln_enp int4 0 0 Contact map
n_fmap5 .aln_enp int4 0 0 Contact map
vis .aln_enp int4 0 0 Visibility property
se_vis .aln_enp int4 0 0 Visibility property
n_vis .aln_enp int4 0 0 Visibility property
name .aln_xxx int1 0 1 Alignment name
enp_list .aln_xxx int4 0 1 List of aligned entities
n_cmp .aln_xxx int4 1 1 Number of aligned entities
l_cmp .aln_xxx int4 1 1 Length of alignment
align_se .aln_xxx int4 0 0 Alignment as sequence refs
rot .aln_xxx flt4 0 1 Rotation matrix [n_cmp-1]
rmsd .aln_xxx flt4 0 1 RMSD [n_cmp*(n_cmp-1)/2]
sim .aln_xxx flt4 0 1 Sequence similarity [n_cmp*(n_cmp-1)/2]
score .aln_xxx flt4 0 1 Alignment raw score [n_cmp*(n_cmp-1)/2]
z .aln_xxx flt4 0 1 Alignment z score [n_cmp*(n_cmp-1)/2]
name .ft int1 0 1 Feature name
group .ft int1 0 1 Feature group name
type .ft int4 0 1 Feature type code
aln .ft int4 1 1 Alignment index in aln_ft
se .ft int4 0 0 List of subentities
n_se .ft int4 1 1 Number of subentities
prop .ft flt4 0 0 Property values
prop_range .ft flt4 0 1 Property range
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Compilation of Similar Sequences
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Name Type Size Mem Description
]]><![CDATA[
ent .cseq int4 1 1 Original (query) entities
name .cseq int1 0 0 Names of similar sequences
iseq .cseq int1 0 0 Similar sequences
se_se .cseq int4 0 0 Alignment
cons_prf .aln_enp int4 0 0 Conservation profile
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Family DB
<![CDATA[
Name Description
]]><![CDATA[
* .aln Structure alignment
* .aln_prop Structure+sequence alignment
* .aln_ft Multiple alignment
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All-to-All Structure Alignment
<![CDATA[
Name Type Size Mem Description
]]><![CDATA[
name .ata int1 0 1 Entity names
aa_cont .ata flt4 0 1 Aminoacid content
rep .ata_dat int4 0 1 Representative assignment
stat .ata_dat int4 0 1 Running statistics
enp .ata_rep int4 1 1 Representative to entity
rep .ata_rep int4 0 1 Represented entities
rep_aln .ata_rep int4 0 1 Represented entities alignment ref
sim .ata_rep int4 0 1 Similar repr
sim_aln .ata_rep int4 0 1 Similar repr alignment ref
enp_list .aln_ata int4 0 0 Alignment repr
z .aln_ata flt4 0 0 Alignment z-score
rmsd .aln_ata flt4 0 0 Alignment rmsd
sim .aln_ata flt4 0 0 Alignment seq sim
trace .aln_ata int4 0 0 Alignment trace
enp .proc int4 0 0 Processor entities
rep_stat .proc int4 0 0 Processor repr used
rep .proc int4 0 0 Processor alignment repr
z .proc flt4 0 0 Processor alignment z-score
rmsd .proc flt4 0 0 Processor alignment rmsd
sim .proc flt4 0 0 Processor alignment seq sim
n_trace .proc int4 0 0 Processor alignment trace size
trace .proc int4 0 0 Processor alignment trace
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Structure Neighbors
<![CDATA[
Name Type Size Mem Description
]]><![CDATA[
name .nb int1 0 1 Entity names
nb .nb int4 0 1 Neighbor entities
nb_aln .nb int4 0 1 Neighbor entities alignment ref
enp_list .aln_nb int4 0 0 Alignment entities
z .aln_nb flt4 0 0 Alignment z-score
rmsd .aln_nb flt4 0 0 Alignment rmsd
sim .aln_nb flt4 0 0 Alignment seq sim
trace .aln_nb int4 0 0 Alignment trace
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