RNA3DB: maintaining a local copy of RNA 3D structure

This package synchronize and curate the updated set of RNA structures from the Protein Data Bank (PDB) ftp site.

Content

[1] script/ scripts and executables for update.

• pdb/derived_data/pdb_seqres.txt.gz FASTA file for all chains (protein and nucleic acid)
• pdb/derived_data/na_seqres.txt FASTA file for all nucleic acid chains
• pdb/derived_data/na_type.list Table of molecule types for nucleic acid chains. This file is in the following format: chain, mol, rna_count, dna_count. rna_count and dna_count are the number of RNA and DNA atoms, respectively. mol is the molecule type decided based on %rna=(rna_count/(rna_count+dna_count)); mol has five values: RNA (%rna=100), RNA/DNA (90%<=%rna<100%), DNA-RNA (10%<%rna<90%), DNA/RNA (0%<%rna<=10%), DNA (%rna=0).
• pdb/derived_data/na_chain.list List RNA chains
• pdb/derived_data/index/resolu.idx Table of resolution

[2] pdb/derived_data/ list and sequence of nucleic acid structures.

[3] pdb/data/structures/all/pdb/ raw PDB files.

[4] cull monomeric PDB chains and their sequences

• cull/pdb_atom.fasta sequences of all chains, converted from "ATOM " record
• cull/pdb_atm.sort.{1.5,2.0,2.5,3.0,3.5,4.0,20.0,all} sequences of all chains up to a certain resolution cutoff
• cull/pdb_atm.sort.{1.5,2.0,2.5,3.0,3.5,4.0,20.0,all}_c{0.8,0.9,1.0}_s{0.0,0.8,0.9,1.0} sequences of cd-hit-est clustered representative sequences with different sequence identity (c) and sequence coverage (s) cutoff
• cull/all_c1.0_s1.0/*.pdb all pdb chains with non-identical sequences
• cull/all_c1.0_s1.0/DSSR/*.dssr DSSR assigned secondary structure

[5] dimer dimeric PDB chains and their sequences, with the same directory structure as cull

Update

Structure database:

script/update.sh

Gene Ontology annotation database (optional):

script/GOA.sh

Statistics of PDB geometry (optional):

script/stat.sh

Results are available under stat