Lab/Institutional Collections
Datasets

X-Ray Diffraction data from Fzd8 CRD complex with DRBP8 DARpin, source of 6NDZ structure

native datasets

X-Ray Diffraction data from Flavin-dependent tryptophan 6-halogenase Thal in complex with 6-bromo-Ltryptophan, source of 9H6N structure

native data

X-Ray Diffraction data from Flavin-dependent tryptophan 7-halogenase RebH in complex with 6-bromo-Ltryptophan, source of 9H6M structure

data with anomalous signal from bromine

X-Ray Diffraction data from c-Src SH3 domain, source of 9OFX structure

X-Ray Diffraction data for c-Src SH3 domain

X-Ray Diffraction data from Patiria miniata Hop1 chromatin binding region, source of 9MYP structure

Zinc anomalous SAD dataset

AF-M predictions accompanying the manuscript: Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions

The set of all AlphaFold multimer (AF-M) v2.3 pairwise structure predictions accompanying the publication: Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions. This dataset includes prediction pairs used for training random forest classifiers including SPOC, pairs used for 30 ranking experiments, all pairs that belong to the genome maintenance matrix on predictomes.org, and three proteome wide in-silico interaction screens conducted with human DONSON, human STK19, and human USP37. All pairs were generated with ColabFold v1.5.2. All our predictions used AF-M multimer version 3 weights models 1, 2, and 4 with 3 recycles, templates enabled, 1 ensemble, no dropout, and no AMBER relaxation. The Multiple Sequence Alignments (MSAs) (unpaired + paired) supplied to AF-M were generated by the MMSeqs2 server using default settings. Sequences run were generally capped at 3,600 amino acids total to avoid memory exhaustion on GPUs.

X-Ray Diffraction data from Schistosoma mansoni Hop1 chromatin binding region, source of 9MUG structure

Zinc SAD dataset

X-Ray Diffraction data from SHP2 tandem SH2 domains in complex with PZR doubly tyrosine phosphorylated ITIM peptide, source of 9MQ5 structure

X-ray diffraction images

HADDOCK docking antibody-antigen models using machine learning-predicted unbound structures

Antibody-antigen models for the paper "Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking". M Giulini, C Schneider, D Cutting, N Desai, C Deane, AMJJ Bonvin. Bioinformatics. 2024

HADDOCK protein-glycan models

Protein-glycan docking models obtained with HADDOCK corresponding to the protocols described in: A Ranaudo, M Giulini, A Pelissou Ayuso, AMJJ Bonvin. Modelling Protein-Glycan Interactions with HADDOCK. Journal of Chemical Information and Modeling (2024)

X-Ray Diffraction data from human polymerase eta with incoming threofuranosyl thymine nucleoside triphosphate opposite DNA dA, source of 9CIQ structure

Crystal structure of human polymerase eta with incoming threofuranosyl thymine nucleoside triphosphate (tTTP) opposite DNA template dA

X-Ray Diffraction data from human polymerase eta with incoming dCMPnPP across O4-methyl threofuranosyl thymidine, source of 9CIH structure

Crystal structure of human polymerase eta with incoming dCMPnPP nucleotide opposite O4-methyl threofuranosyl thymidine in DNA template at extension stage

X-Ray Diffraction data from human polymerase eta with incoming dAMPnPP opposite O4-methyl threofuranosyl thymidine, source of 9CJ9 structure

Crystal structure of human polymerase eta with incoming dAMPnPP nucleotide opposite O4-methyl threofuranosyl thymidine in DNA template

X-Ray Diffraction data from Human Polymerase eta with incoming dAMPnPP nucleotide opposite threofuranosyl thymidine, source of 9CHW structure

Crystal structure of human polymerase eta with incoming dAMPnPP nucleotide opposite threofuranosyl thymidine modified DNA template

X-Ray Diffraction data from Hen egg-white lysozyme (HEWL), source of structure

A series of 3049 pink-beam, polychromatic still images spaced one degree between adjacent frames. Metadata: Detector distance: 200 mm Beam center: (176.22 mm, 174.68 mm) Peak wavelength: 1.05 Angstroms Bandwidth: 5.5% (BioCARS) Unit cell constants: 79.405, 79.405, 37.837, 90.00, 90.00, 90.00 Space group: P43212

X-Ray Diffraction data from E. coli dihydrofolate reductase bound to NADP+ and folate, source of structure

A series of 180 pink-beam, polychromatic still images spaced one degree between adjacent images. Metadata: Detector distance: 200 mm Beam center: (176.00 mm, 173.93 mm) Peak wavelength: 1.05 Angstroms Beam spectral bandwidth: 5.5% (BioCARS) Unit cell: 34.297, 45.552, 99.035, 90, 90, 90 Space group: P212121

X-Ray Diffraction data from Second PDZ domain of Ligand of Numb protein X 2 (human), source of 5E11 structure

Time-resolved data consisting of four passes of pink still images for PDZ2. Passes C, D, and E are spaced two degrees between adjacent images, with pass F spaced one degree between adjacent images. Start angles are 0, 92, 181, and 361.5 degrees for passes C, D, E, and F respectively. Time points are collected at 0, 50, 100, and 200 nanoseconds per image per pass. Metadata: Detector distance: 200 mm Beam center: (175.76 mm, 154.17 mm) Peak wavelength: 1.04 Angstroms Beam spectral bandwidth: 5.5% (BioCARS) Unit cell: 65.3, 39.45, 39.01, 90, 117.54, 90 Space group: C121 Applied voltage: 6.01 kV

X-Ray Diffraction data from flavin reductase ThdF in complex with NAD and FAD, source of 9FD6 structure

native data

X-Ray Diffraction data from flavin reductase ThdF in complex with two bound FADs, source of 9FD5 structure

native data

X-Ray Diffraction data from flavin reductase ThdF in complex with two bound FADs, source of 9FD4 structure

native data