Jan 10, 2022 · We explore what AlphaFold2 has memorized and learned, and describe specific examples that highlight differences compared to state-of-the-art peptide docking protocol …

Feb 4, 2025 · Prior studies have demonstrated that AF-multimer (AFm) can predict accurate protein complexes in only up to 43% of cases. 1 In this work, we combine AlphaFold as a …

On the other hand, Wong et al. 57 developed a model to predict protein-ligand interactions based on AF structures and molecular docking and indicated, contrary to our results, that "molecular …

Here, we combine AlphaFold2 with molecular docking simulations to predict protein-ligand interactions between 296 proteins spanning Escherichia coli's essential proteome, and 218 …

Sep 13, 2023 · AlphaFold2 (AF2) has provided renewed hope for improvements in the field of protein–protein docking but has shown limited success against antibody-antigen complexes …

AlphaFold 2 (AF2) was the star of CASP14, the last biannual structure prediction experiment. Using novel deep learning, AF2 predicted the structures of many difficult protein targets at or …

Sep 14, 2024 · The results show that the Glide_SFCT (PS) pipeline exhibited the best target prediction performance based on the atomic structure models in AlphaFold2 human proteome. …

Sep 7, 2021 · It has been demonstrated earlier that the neural network based program AlphaFold2 can be used to dock proteins given the two sequences separated by a gap as the input. The …

Sep 15, 2021 · Here, we examine the use of AlphaFold2 (AF2) for predicting the structure of heterodimeric protein complexes. We find that using the default AF2 protocol, 44% of the …

AlphaFold2 is a promising new tool for researchers to predict protein structures and generate high-quality models, with low backbone and global root-mean-square deviation (RMSD) when …

Jan 20, 2023 · Recently, AlphaFold (AF), an artificial-intelligence-based protein structure prediction method, has shown impressive results in terms of model accuracy. This outstanding …

Mar 13, 2025 · 1 Introduction. Since 2020, AlphaFold2 [AF2 (Evans et al. 2021, Jumper et al. 2021)] and other similar deep learning algorithms (Baek et al. 2023, Ahdritz et al. 2024) have …

Jan 10, 2022 · Our simple implementation of AlphaFold2 generates peptide-protein complex models without requiring multiple sequence alignment information for the peptide partner, and …

We explore what AlphaFold2 has memorized and learned, and describe specific examples that highlight differences compared to state-of-the-art peptide docking protocol PIPER-FlexPepDock.

3 days ago · To search for candidates among the 38,700 representative viral proteins that directly interact with ThsA or ThsB in the bacterial type I Thoeris system, the authors used AlphaFold2 …

Mar 16, 2025 · A protein language model called ProGen was trained to produce protein sequences with a predictable function across diverse protein families. ... (an online tool …

In this study, the ability of AlphaFold to predict which peptides and proteins interact, as well as its accuracy in modeling the resulting interaction complexes, are benchmarked against …

AlphaFold is a machine learning model for the prediction of protein folding.. This page discusses how to use AlphaFold v2.0, the version that was entered in CASP14 and published in Nature. …

Jul 27, 2022 · It has been demonstrated earlier that the neural network based program AlphaFold2 can be used to dock proteins given the two sequences separated by a gap as the …

Mar 14, 2025 · Crampon K, Giorkallos A, Deldossi M, Baud S, Steffenel LA. Machine-learning methods for ligand–protein molecular Docking. Drug Discovery Today. 2022;27:151–64. Article …

The results show that the Glide_SFCT (PS) pipeline exhibited the best target prediction performance based on the atomic structure models in AlphaFold2 human proteome. It …

8 hours ago · Bottom: Strep-Tactin beads loaded with purified AfAFP-F-S, PgAFP-F-S, and F-S proteins. C In silico docking simulations using AlphaFold2 multimer to analyze interactions …

1 day ago · 1 Introduction. Alpha-amylase (α-amylase, EC 3.2.1.1), a member of the glycoside hydrolase family 13, is the second most widely used enzyme in the world, representing …

3 days ago · PRRX1 interacts with Ku70. (A) Proteins identified by IP of FLAG-PRRX1 followed by MS in glioblastoma cells.Components of the NHEJ core complex and PRRX1 are listed. …