AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

M Varadi, D Bertoni, P Magana, U Paramval… - Nucleic acids …, 2024 - academic.oup.com
Abstract The AlphaFold Database Protein Structure Database (AlphaFold DB,
https://alphafold. ebi. ac. uk) has significantly impacted structural biology by amassing over …

Recent advances and challenges in protein structure prediction

CX Peng, F Liang, YH Xia, KL Zhao… - Journal of Chemical …, 2023 - ACS Publications
Artificial intelligence has made significant advances in the field of protein structure prediction
in recent years. In particular, DeepMind's end-to-end model, AlphaFold2, has demonstrated …

[HTML][HTML] Apprehensions and emerging solutions in ML-based protein structure prediction

KM Dahlström, TA Salminen - Current Opinion in Structural Biology, 2024 - Elsevier
The three-dimensional structure of proteins determines their function in vital biological
processes. Thus, when the structure is known, the molecular mechanism of protein function …

The impact of AI‐based modeling on the accuracy of protein assembly prediction: Insights from CASP15

B Ozden, A Kryshtafovych… - … : Structure, Function, and …, 2023 - Wiley Online Library
In CASP15, 87 predictors submitted around 11 000 models on 41 assembly targets. The
community demonstrated exceptional performance in overall fold and interface contact …

The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions

B Jiménez-García, J Roel-Touris… - Nucleic acids …, 2023 - academic.oup.com
Computational docking is an instrumental method of the structural biology toolbox.
Specifically, integrative modeling software, such as LightDock, arise as complementary and …

[HTML][HTML] Channel Formation in Cry Toxins: An Alphafold-2 Perspective

J Torres, W Surya, P Boonserm - International journal of molecular …, 2023 - mdpi.com
Bacillus thuringiensis (Bt) strains produce pore-forming toxins (PFTs) that attack insect pests.
Information for pre-pore and pore structures of some of these Bt toxins is available. However …

[HTML][HTML] Rosetta Energy Analysis of AlphaFold2 models: Point Mutations and Conformational Ensembles

RA Stein, HS Mchaourab - bioRxiv, 2023 - ncbi.nlm.nih.gov
There has been an explosive growth in the applications of AlphaFold2, and other structure
prediction platforms, to accurately predict protein structures from a multiple sequence …

[HTML][HTML] SERPINC1 c.1247dupC: a novel SERPINC1 gene mutation associated with familial thrombosis results in a secretion defect and quantitative antithrombin …

M Ruf, S Cunningham, A Wandersee, R Brox… - Thrombosis …, 2024 - Springer
Background Antithrombin (AT) is an important anticoagulant in hemostasis. We describe
here the characterization of a novel AT mutation associated with clinically relevant …

[HTML][HTML] Protein structure and dynamics in the era of integrative structural biology

R Grandori - Frontiers in Biophysics, 2023 - frontiersin.org
Proteins carry out their biological activity as dynamic structures and populate in solution or in
biological membranes structural distributions with different degrees of heterogeneity. The …

[HTML][HTML] The path to solving the protein folding problem

J Straiton - 2023 - Taylor & Francis
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