AFDB comparison

Do heuristic search of query structure against a cropped AlphaFold database (AFDB2), ignoring low confidence regions of models in AFDB2. Cropping removes residues from AlphaFold models that have pLDDT<60. Example output

STEP 1 - Enter your query protein structure

Structures must be specified by Dali's internal AFDB2 structure identifiers (e.g., fbuzA) or by concatenating the PDB identifier (4 characters) and a chain identifier (1 character). Or, you may upload a structure in PDB format.

OR upload file

STEP 2 - Select target proteins or taxon

Choose: Select Target Vertebrate proteomes in AFDB2 Human Mouse Rat Zebrafish Invertebrate proteomes in AFDB2 Fruit fly Nematode worm Leishmania Plasmodium falciparum Trypanosoma cruzi Dictyostelium (amoeba) Trypanosoma brucei Brugia malayi Dracunculus medinensis Onchocerca volvulus Schistosoma mansoni Strongyloides stercoralis Trichuris trichiura Wuchereria bancrofti Plant proteomes in AFDB2 Arabidopsis thaliana Maize Rice Soybean Fungal proteomes in AFDB2 Budding yeast Fission yeast Candida albicans Ajellomyces capsulatus Cladophialophora carrionii Fonsecaea pedrosoi Madurella mycetomatis Paracoccidioides lutzii Sporothrix schenckii Prokaryotic proteomes in AFDB2 Escherichia coli Enterococcus faecium Campylobacter jejuni Haemophilus influenzae Helicobacter pylori Klebsiella pneumoniae Mycobacterium leprae Mycobacterium ulcerans Mycobacterium tuberculosis Methanococcus jannaschii Neisseria gonorrhoeae Nocardia brasiliensis Pseudomonas aeruginosa Salmonella typhimurium Shigella dysenteriae Staphylococcus aureus Streptococcus pneumoniae BFVD (no Dali identifiers as query) AlphaFold Database (AFDB2) Swissprot proteins in AFDB2 Proteomes in AFDB2

STEP 3 - Choose search mode

Heuristics are used to prioritize potential matches in the AFDB2 database. 'Quicker' validates a small number of candidates, returning a sample of similar structures. 'Slower' validates a moderate number of candidates, returning more high scoring similarities.

Quicker Slower

STEP 4 - Optional data

You may leave an e-mail address for notification when the job has finished. The job title is used as subject heading in the e-mail.

STEP 5 - Submit your job

Report bugs to liisa dot holm at helsinki dot fi