There is still a long way to go to grasp the complexity of protein-ligand interactions fully, but leveraging deep learning for structure prediction of the entire complex may bring us one step closer to the solution. Methods PDBbind We used PDBbind from 2019 (2020 release29) processed by the...
Improvements of protein complex structure prediction To examine the impact of DeepMSA2-Multimer on protein complex structure modeling, we collected 54 complex targets from CASP13 and CASP14 each of which contains between two and eight chains; 40 of the targets are homomers and 14 are heteromeric...
H Chen,HX Zhou - 《Proteins Structure Function & Bioinformatics》 被引量: 422发表: 2010年 3D Complex: A Structural Classification of Protein Complexes Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical prop...
TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment Even with the significant advances of AlphaFold-Multimer (AF-Multimer) and AlphaFold3 (AF3) in protein complex structure prediction, their accuracy is stil... B Han,Y Zhang,L Li,... ...
predictionasAhmadandMizuguchi[29]demonstratedthatpartner-specificinterfacepredictors yieldmuchhigherperformance.Pairedinterfacepredictionisalsoofimportancetoprotein–protein docking,thecomputationaltaskofpredictingthethree-dimensionalstructureofacomplexfrom itsindividualproteins.Dockingsoftwarecurrentlyachieveslowaccuracy[30]:...
neuralplexer-inference --task=batched_structure_sampling \ --input-receptor input.pdb \ --input-ligand <ligand>.sdf \ --use-template --input-template <template>.pdb \ --out-path \ --model-checkpoint <data_dir>/models/complex_structure_prediction.ckpt \ --n-samples 16 \ --chunk-size...
(3D) structure of protein complexes and protein-protein interfaces. A single protein can be involved in variety of protein complexes. Same complex can perform different functions depending on several factors such as, stage of cell cycle, the nutritional status of the cell, the cellular compartment...
De novo protein design by inversion of the AlphaFold structure prediction network Casper Goverde, Benedict Wolf, Hamed Khakzad, Stephane Rosset, Bruno E Correia bioRxiv 2022.12.13.520346 • code • lecture1 • lecture2 Code of OpenComplex Jingcheng, Yu and Zhaoming, Chen and Zhaoqun, Li an...
Methods that require the structure of both proteins in a complex to make a prediction are called partner-specific, and methods that can make interface predictions on individual unbound proteins are referred to as partner-independent. Some template-free methods, like ISPRED4 [24], are partner-inde...
Super-secondary structure is simply a combination of secondary structures. Consider a piece of paper; if it were rolled into a tube, it would still be a piece of paper, but it would have been modified into amore complex structure. The same can be done to a β-sheet, and in this cas...