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Folddisco

Folddisco is a bioinformatics tool for indexing and searching for discontinous motifs in protein structures.

Command

Installation

# Default
cargo install --features foldcomp --path .

Indexing

# default for small databases
folddisco index -p <PDB_DIR|FOLDCOMP_DB> -i <INDEX_PATH> -t <THREADS> 
# For large databases (number of structures > 65536). This will generate a 8GB fixed-size offset file
folddisco index -p <PDB_DIR|FOLDCOMP_DB> -i <INDEX_PATH> -t <THREADS> -m big

# Setting the number of bins and feature
folddisco index -p <PDB_DIR|FOLDCOMP_DB> -i <INDEX_PATH> -t <THREADS> -d <DISTANCE_BINS> -a <ANGLE_BINS> -y <FEATURE_TYPE>
# Example
# Indexing human proteome with 12 threads
folddisco index -p h_sapiens -i index/h_sapiens_folddisco -t 12

You can also download pre-built index files

Querying

# default
folddisco query -i <INDEX> -p <QUERY_PDB> -q <QUERY_RESIDUES> -r -t <THREADS>
# -r flag is for residue matching & rmsd calculation
# -v flag is for verbose output (measures step-by-step runtime)

# Using the whole structure as a query
folddisco query -i <INDEX> -p <QUERY_PDB> -r -t <THREADS>

# Using query.txt file
folddisco query -i <INDEX> -q <QUERY_FILE> -r -t <THREADS>

# Using distance and angle threshold
folddisco query -i <INDEX> -p <QUERY_PDB> -q <QUERY_RESIDUES> -d <DISTANCE_THRESHOLD> -a <ANGLE_THRESHOLD> -r -t <THREADS>
# Example
# Zinc finger query to human proteome
folddisco query -i index/h_sapiens_folddisco -p query/1G2F.pdb -q F207,F212,F225,F229 -r -d 0.5 -a 5 -t 12
folddisco query -i index/h_sapiens_folddisco -q query/zinc_finger.txt -r -d 0.5 -a 5 -t 12

# Serine protease query to human proteome
folddisco query -i index/h_sapiens_folddisco -p query/4CHA.pdb -q B57,B102,C195 -r -t 12
folddisco query -i index/h_sapiens_folddisco -q query/serine_protease.txt -r -t 12

Index list

  • index/
    • h_sapiens_folddisco: Human proteome, 23K structures
    • e_coli_folddisco: E. coli proteome, 4K structures

Example query list

  • query/
    • 1G2F.pdb: Zinc finger protein
    • 4CHA.pdb: Serine protease
    • 1LAP.pdb: Aminopeptidase
    • zinc_finger.txt: 1G2F.pdb F207,F212,F225,F229
    • serine_protease.txt: 4CHA.pdb B57,B102,C195
    • aminopeptidase.txt: 1LAP.pdb 250,255,273,332,334
    • knottin.txt: 2N6N.pdb 3,10,15,16,21,23,28,30

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