Foldseek enables fast and sensitive comparisons of large structure sets.
van Kempen M, Kim S, Tumescheit C, Mirdita M, Söding J, and Steinegger M. Foldseek: fast and accurate protein structure search. bioRxiv, doi:10.1101/2022.02.07.479398 (2022)
We presented a Foldseek tutorial at the SBGrid where we demonstrate the webserver and command line interface of foldseek. Check it out here.
Search your protein structures against the AlphaFoldDB and PDB in seconds using our Foldseek webserver: search.foldseek.com
# static Linux AVX2 build (check using: cat /proc/cpuinfo | grep avx2) wget https://mmseqs.com/foldseek/foldseek-linux-avx2.tar.gz; tar xvzf foldseek-linux-avx2.tar.gz; export PATH=$(pwd)/foldseek/bin/:$PATH # static Linux SSE4.1 build (check using: cat /proc/cpuinfo | grep sse4_1) wget https://mmseqs.com/foldseek/foldseek-linux-sse41.tar.gz; tar xvzf foldseek-linux-sse41.tar.gz; export PATH=$(pwd)/foldseek/bin/:$PATH # static macOS build (universal binary with SSE4.1/AVX2/M1 NEON) wget https://mmseqs.com/foldseek/foldseek-osx-universal.tar.gz; tar xvzf foldseek-osx-universal.tar.gz; export PATH=$(pwd)/foldseek/bin/:$PATH # conda installer conda install -c conda-forge -c bioconda foldseek
Other precompiled binaries for ARM64, PPC64LE amd SSE2 are available at https://mmseqs.com/foldseek.
easy-search can search single or multiple query structures formatted in PDB/mmCIF format (flat or
.gz) against a target database (
example/) of protein structures. It outputs a tab-separated file of the alignments (
.m8) the fields are
foldseek easy-search example/d1asha_ example/ aln.m8 tmpFolder
Output: Customize fields of tab seperated output
The output can be customized with the
--format-output option e.g.
--format-output "query,target,qaln,taln" returns the query and target accession and the pairwise alignments in tab separated format. You can choose many different output columns.
query Query sequence identifier target Target sequence identifier evalue E-value gapopen Number of gap open events (note: this is NOT the number of gap characters) pident Percentage of identical matches fident Fraction of identical matches nident Number of identical matches qstart 1-indexed alignment start position in query sequence qend 1-indexed alignment end position in query sequence qlen Query sequence length tstart 1-indexed alignment start position in target sequence tend 1-indexed alignment end position in target sequence tlen Target sequence length alnlen Alignment length (number of aligned columns) raw Raw alignment score bits Bit score cigar Alignment as string. Each position contains either M (match), D (deletion, gap in query), or I (Insertion, gap in target) qseq Query sequence tseq Target sequence qaln Aligned query sequence with gaps taln Aligned target sequence with gaps qheader Header of Query sequence theader Header of Target sequence mismatch Number of mismatches qcov Fraction of query sequence covered by alignment tcov Fraction of target sequence covered by alignment empty Dash column '-' taxid Taxonomical identifier (needs mmseqs tax db) taxname Taxon Name (needs mmseqs tax db) taxlineage Taxonomical lineage (needs mmseqs tax db) qset Query filename of FASTA/Q (useful if multiple files were passed to createdb) qsetid Numeric identifier for query filename tset Target filename of FASTA/Q (useful if multiple files were passed to createdb) tsetid Numeric identifier for target filename qca Calpha corrdinates of the query tca Calpha corrdinates of the target alntmscore TM-score of the alignment qtmscore TM-score normalized by the query length ttmscore TM-score normalized by the target length u Rotation matrix (computed to by TM-score) t Translation vector (computed to by TM-score) lddt Average LDDT of the alignment lddtfull LDDT per aligned position
Output: Superpositioned Cα only PDB files
--format-mode 5 generates PDB files with all Cα atoms superimposed based on the aligned coordinates on to the query structure.
For each pairwise alignment it will write a single PDB files, so be carefull when using this options for large searches.
Create reusable databases and indexes
The target database can be pre-processed by
createdb. This make sense if searched multiple times.
foldseek createdb example/ targetDB foldseek createindex targetDB tmp #OPTIONAL generates and stores the index on disk foldseek easy-search example/d1asha_ targetDB aln.m8 tmpFolder
Important search parameters
# sensitivity and speed -s adjust the sensitivity to speed trade-off. lower is faster, higher more sensitive (fast: 7.5, highest sensitivity (default): 9.5) --exhaustive-search skips the prefilter and performs an all-vs-all alignment (more sensitive but much slower) --max-seqs adjust the amount of prefilter that are handed to the alignment. Increasing it can lead to more hits (default: 1000) -e List matches below this E-value (range 0.0-inf, default: 0.001) Increasing it helps to report more distantly related structures. Structures with an E-value of up to 1 might be still related. # other --alignment-type 0: 3Di Gotoh-Smith-Waterman (local, not recommended), 1: TMalign (global, slow), 2: 3Di+AA Gotoh-Smith-Waterman (local, default) -c list matches above this fraction of aligned (covered) residues (see --cov-mode) (default: 0.0) The higher the alignment coverage the more global is the alignment. --cov-mode 0: coverage of query and target, 1: coverage of target, 2: coverage of query
databases command downloads pre-generated databases like PDB or AlphaFoldDB.
# pdb foldseek databases PDB100 pdb tmp # alphafold db foldseek databases Alphafold/Proteome afdb tmp
We currently support the following databases:
Name Type Taxonomy Url - Alphafold/UniProt Aminoacid yes https://alphafold.ebi.ac.uk/ - Alphafold/UniProt50 Aminoacid yes https://alphafold.ebi.ac.uk/ - Alphafold/Proteome Aminoacid yes https://alphafold.ebi.ac.uk/ - Alphafold/Swiss-Prot Aminoacid yes https://alphafold.ebi.ac.uk/ - ESMAtlas30 Aminoacid - https://esmatlas.com - PDB Aminoacid yes https://www.rcsb.org
easy-searchfast protein structure search
createdbcreate a database from protein structures (PDB,mmCIF, mmJSON)
databasesdownload pre-assembled databases
Using TMalign for the alignment
Foldseek supports to realign hits using TMalign as well as rescoring alignments using TMscore.
foldseek easy-search example/d1asha_ example/ aln tmp --alignment-type 1
In case of the alignment type (
--alignment-type 1) tmalign we sort the results by the TMscore normalized by query length. We write the TMscore into the e-value(=TMscore) as well as into the score(=TMscore*100) field.
Rescore aligments using TMscore
Easiest way to get the alignment TMscore normalized by min(alnLen,qLen,targetLen) as well as a rotation matrix is through the following command:
foldseek easy-search example/ example/ aln tmp --format-output query,target,alntmscore,u,t
Alternative, it is possible to compute TMscores for the kind of alignment output (e.g. 3Di/AA) using the following commands:
foldseek createdb example/ targetDB foldseek createdb example/ queryDB foldseek search queryDB targetDB aln tmpFolder -a foldseek aln2tmscore queryDB targetDB aln aln_tmscore foldseek createtsv queryDB targetDB aln_tmscore aln_tmscore.tsv
aln_tmscore.tsv: query and target identifier, TMscore, translation(3) and rotation vector=(3x3)
Search result visualisations
Foldseek can locally generate a search result HTML similiar to the webserver by specifying the format mode
foldseek easy-search example/d1asha_ example/ result.html tmp --format-mode 3
The following command aligns the input structures all-against-all and keeps only alignments with 80% of the sequence covered by the alignment (-c 0.8) (read more about alignment coverage here). It then clusters the results using greedy set cover algorithm. The clustering mode can be adjusted using --cluster-mode, read more here. The clustering output format is described here.
foldseek createdb example/ db foldseek search db db aln tmpFolder -c 0.8 foldseek clust db aln clu foldseek createtsv db db clu clu.tsv
Query centered multiple sequence alignment
Foldseek can generate a3m based multiple sequence alignments using the following commands.
a3m can be converted to fasta format using reformat.pl (
reformat.pl in.a3m out.fas).
foldseek createdb example/ targetDB foldseek createdb example/ queryDB foldseek search queryDB targetDB aln tmpFolder -a foldseek result2msa queryDB targetDB aln msa --msa-format-mode 6 foldseek unpackdb msa msa_output --unpack-suffix a3m --unpack-name-mode 0
Compile from source
foldseek from source has the advantage of system-specific optimizations, which should improve its performance. To compile it
g++ (4.9 or higher) and
cmake (3.0 or higher) are required. Afterwards, the foldseek binary will be located in the
git clone https://github.com/steineggerlab/foldseek.git cd foldseek mkdir build cd build cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. .. make -j make install export PATH=$(pwd)/foldseek/bin/:$PATH
foldseek on macOS, please install and use
gcc from Homebrew. The default macOS
clang compiler does not support OpenMP (by default) and
foldseek will not be able to run multi-threaded. Adjust the
cmake call above to:
CC="$(brew --prefix)/bin/gcc-11" CXX="$(brew --prefix)/bin/g++-11" cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..