Protein complex prediction with AlphaFold-Multimer
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Summary
This work demonstrates that an AlphaFold model trained specifically for multimeric inputs of known stoichiometry, which it is called AlphaFolding-Multimer, significantly increases accuracy of predicted multimerics interfaces over input-adapted single-chain AlphaFolds while maintaining high intra-chain accuracy.
- Type
- preprint
- Published
- 2021-10-04
- Cited by
- 3,312
- References
- 46
- Access
- Open access
- OpenAlex
- https://openalex.org/W3202105508
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:238413014
Keywords
Homomeric, Benchmark (surveying), Computer science, Template, Linker
References
- Detection of gene pathways with predictive power for breast cancer prognosis
- Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex
- Hidden Markov model speed heuristic and iterative HMM search procedure
- TM-align: a protein structure alignment algorithm based on the TM-score
- Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
- Sequence co-evolution gives 3D contacts and structures of protein complexes
- ZDOCK: An initial‐stage protein‐docking algorithm
- SwarmDock: a server for flexible protein-protein docking
- Mapping Monomeric Threading to Protein–Protein Structure Prediction
- Detecting putative orthologs
- DockQ: A Quality Measure for Protein-Protein Docking Models
- The ClusPro web server for protein-protein docking
- Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology
- Larval Dispersal of Spodoptera frugiperda Strains on Bt Cotton: A Model for Understanding Resistance Evolution and Consequences for its Management
- Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis
- ComplexContact: a web server for inter-protein contact prediction using deep learning
- Protein Data Bank: the single global archive for 3D macromolecular structure data
- SCL/TAL1 cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells
- Clustering huge protein sequence sets in linear time
- Protein interaction networks revealed by proteome coevolution
Cited by
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- Use of High Pressure NMR Spectroscopy to Rapidly Identify Proteins with Internal Ligand-Binding Voids
- Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles
- A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and sidechain flexibility
- DIPS-Plus: The enhanced database of interacting protein structures for interface prediction
- Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4
- Molecular mechanisms of stress-induced reactivation in mumps virus condensates
- Harnessing protein folding neural networks for peptide–protein docking
- Determinants shaping the nanoscale architecture of the mouse rod outer segment
- From complete cross-docking to partners identification and binding sites predictions
- RAPPPID: Towards Generalisable Protein Interaction Prediction with AWD-LSTM Twin Networks
- ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction
- Transmembrane region dimer structures of Type 1 receptors readily sample alternate configurations: MD simulations using the Martini 3 coarse grained model compared to AlphaFold2 Multimer
- Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26
- Moving beyond content‐specific computation in artificial neural networks
- Protein-protein interaction-Gaussian accelerated molecular dynamics (PPI-GaMD): Characterization of protein binding thermodynamics and kinetics
- AI revolutions in biology
- AlphaDesign: A de novo protein design framework based on AlphaFold
- Inverse Potts model improves accuracy of phylogenetic profiling
- Identification of Iron-Sulfur (Fe-S) and Zn-binding Sites Within Proteomes Predicted by DeepMind’s AlphaFold2 Program Dramatically Expands the Metalloproteome
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