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 …

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. …

Mar 18, 2025 · The ability of AlphaFold2 multimer to accurately predict the bound conformation for the protein-protein homo and heteromer complex has surpassed the performance of docking …

1 day ago · 1 INTRODUCTION. AlphaFold2 (AF2) is a deep-learning-based algorithm that predicts a protein's three-dimensional structure from its amino acid sequence, often with high …

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 …

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 …

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 …

Sep 6, 2022 · We combined protein structure predictions from AlphaFold2 with docking to predict protein‐ligand interactions between active and inactive antibacterial compounds found in a …

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

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

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.

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 …

5 days ago · We introduce AlphaFold2-RAVE (af2rave), an open-source Python package that integrates machine learning-based structure prediction with physics-driven sampling to …

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 …

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 …

1 day ago · To screen mutants with enhanced activity, a semi-rational design approach was employed based on sequence and structural information of TfGT. Initially, the protein structure …

Mar 14, 2023 · AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind that can predict three-dimensional (3D) structures of proteins from amino acid sequences with …

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 …

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. …

1 day ago · The quantum electrodynamical phaseless auxiliary-field quantum Monte Carlo (QED-AFQMC) method can simulate the interaction between the vacuum fluctuations of cavity …

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 …

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 …

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 …

1 day ago · Halophilic bacteria thrive in high-salt environments through structural modifications in their proteins. One such adaptation is seen in the DNA polymerase III beta subunit, which acts …

1 day ago · A modeled dimeric structure of Anc05 predicted using Alphafold2 (Jumper et al. 2021). The subunits of the proteins are each colored differently. Credit: Protein Science (2025).

Mar 19, 2025 · The conserved centriole/centrosome protein Spd-2/CEP192 (fly/human nomenclature) plays an important part in mitotic centrosome assembly in humans (17, 18), flies …