Lab/Institutional Collections
Datasets

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.

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

X-Ray Diffraction data from Human p120RasGAP, C2 and GAP domains, source of 9BZ4 structure

Native datasets

X-Ray Diffraction data from methyltransferase MpaG' in complex with SAH and FDHMP-3C, source of 8XTF structure

Mycophenolic acid biosynthesis cluster protein G' in complex with SAH and FDHMP-3C

X-Ray Diffraction data from methyltransferase MpaG' in complex with SAH and FDHMP, source of 8XTE structure

Mycophenolic acid biosynthesis cluster protein G' in complex with SAH and FDHMP

X-Ray Diffraction data from methyltransferase MpaG' in complex with SAH and DMMPA, source of 8XTG structure

Mycophenolic acid biosynthesis cluster protein G' in complex with SAH and DMMPA

X-Ray Diffraction data from EGFRvIII extracellular region in complex with VHH 34E5, source of 8UKV structure

Native Dataset

X-Ray Diffraction data from EGFRvIII extracellular region, source of 8UKX structure

Native Dataset

X-Ray Diffraction data from EGFRvIII extracellular region, source of 8UKW structure

Native dataset