Protein contact prediction
Webb7 apr. 2024 · We introduce TemPL, a novel deep learning approach for zero-shot prediction of protein stability and activity, harnessing temperature-guided language modeling. By assembling an extensive dataset of ten million sequence-host bacterial strain optimal growth temperatures (OGTs) and ΔTm data for point mutations under consistent … WebbIdentification of protein-protein interactions (PPIs) plays an essential role in the understanding of protein functions and cellular biological activities. However, the …
Protein contact prediction
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WebbDefinition. Predicting the tertiary structure of a protein by looking at its amino acid (i.e., primary) sequence is usually called the protein folding problem. Contact map structures are bidimensional objects representing some of the structural information of a protein. In this contribution, we treat the use of contact map predictions to ... Webb15 dec. 2024 · Awesome protein structure prediction (PSP) methods We recently released a review about PSP models, named Protein Language Models and Structure Prediction: Connection and Progression, which aims to build the connections between pLMs and PSP, and recover the PSP methods: past, present, and future.
WebbFor the top 1, 10 and 100 predicted contacts, DeepHomo obtained the accuracies of 62.3%, 52.6% and 37.6%, re- spectively, compared with 27.0%, 15.6% and 5.2% for DCA DI and 33.0%, 22.2% and 8.1% for DCA APC. Similar advantages of DeepHomo over DCA-based approaches can also be observed in the success rate of contact prediction. Webb10 juni 2024 · Interchain protein contact predictions are not only useful to identify protein–protein interactions but also in the construction of complex structures.
WebbMotivation Fast and accurate prediction of protein-ligand binding structures is indispensable for structure-based drug design and accurate estimation of binding free energy of drug candidate molecules in drug discovery. Recently, accurate pose prediction methods based on short Molecular Dynamics (MD) simulations, such as MM-PBSA and … Webb8 jan. 2024 · Accurate prediction of contacting residue pairs between interacting proteins is very useful for structural characterization of protein-protein interactions (PPIs). …
WebbWe have developed the residue-level protein graph based on 3D protein structures generated by AlphaFold. 13 Approximately 50% of the proteins in both datasets have …
Webb10 dec. 2013 · A group graphical lasso (GGL) method for contact prediction that integrates joint multi-family EC analysis and supervised learning to improve accuracy on proteins without many sequence homologs and can also integrate supervised learning methods to further improve accuracy. MOTIVATION Protein contact prediction is important for … lakeland 33812Webb29 juli 2024 · Similarly, in the protein contact prediction problem, the output is a contact probability map (matrix) of size L × L and input is protein features of dimension L × L × N, … jene bankWebb22 maj 2024 · The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that … lakeland 3 dayWebb13 feb. 2024 · It is found that the knowledge learned by a protein-coevolution Transformer-based deep neural network can be transferred to the RNA contact prediction task and the resulting framework greatly reduce the data scarcity bottleneck. RNA, whose functionality is largely determined by its structure, plays an important role in many biological activities. lakeland 50 2023Webb8 jan. 2024 · Extensive evaluation on multiple test sets shows that PLMGraph-Inter significantly outperforms three top inter-protein contact prediction methods, including … jene bijlsWebbIdentification of protein-protein interactions (PPIs) plays an essential role in the understanding of protein functions and cellular biological activities. However, the traditional experiment-based methods are time-consuming and laborious. Therefore, developing new reliable computational approaches has great practical significance for … jenebe grupWebbför 2 dagar sedan · Quantification of how different environmental cues affect protein allocation can provide important insights for understanding cell physiology. While … je ne bois