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History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics
Prof. Haruki Nakamura, who is the former head of Protein Data Bank Japan (PDBj) and an expert in computational biology, retired from Osaka...
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Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future
As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by...
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The Protein Data Bank Archive
Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure data. Established in 1971 as the first open...
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Belowground organs and bud bank: Insights on morphoanatomical functional traits related to fire
The presence of belowground organs with buds and carbohydrate storage is typical of perennial plants in fire-prone ecosystems. The bud-bearing...
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TUPDB: Target-Unrelated Peptide Data Bank
The isolation of target-unrelated peptides (TUPs) through biopanning remains as a major problem of phage display selection experiments. These TUPs do...
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Databases and Protein Structures
Bioinformatics databases contain biological data from scientific experiments, most importantly DNA and protein sequences and protein structures....
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Determining Protein Structures Using X-Ray Crystallography
X-ray crystallography is a robust and widely used technique that facilitates the three-dimensional structure determination of proteins at an atomic...
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Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data
BackgroundMachine learning (ML) has a rich history in structural bioinformatics, and modern approaches, such as deep learning, are revolutionizing...
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Genetic diversity and selection signatures in a gene bank panel of maize inbred lines from Southeast Europe compared with two West European panels
Southeast Europe (SEE) is a very important maize-growing region, comparable to the Corn belt region of the United States, with similar dent germplasm...
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Modeling of Protein Complexes
The recent advances in structural biology, combined with continuously increasing computational capabilities and development of advanced softwares,...
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Protein-Protein Interaction Studies Using Molecular Dynamics Simulation
Protein-protein interactionProtein-protein interaction (PPI) is a crucial event for many biological functions. Studying the molecular details of PPI...
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CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2
Deep learning models, such as AlphaFold2 and RosettaFold, enable high-accuracy protein structure prediction. However, large protein complexes are...
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Generation of a bank of clinical-grade, HLA-homozygous iPSC lines with high coverage of the Spanish population
BackgroundInduced pluripotent stem cell (iPSC)-derived cell therapies are an interesting new area in the field of regenerative medicine. One of the...
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Data-driven regularization lowers the size barrier of cryo-EM structure determination
Macromolecular structure determination by electron cryo-microscopy (cryo-EM) is limited by the alignment of noisy images of individual particles....
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Genomic prediction of zinc-biofortification potential in rice gene bank accessions
Key messageA genomic prediction model successfully predicted grain Zn concentrations in 3000 gene bank accessions and this was verified...
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Drug Design Methods to Regulate Protein–Protein Interactions
Inhibiting anomalous protein–protein interactions has led to the discovery of drugs (small molecules, precisely) that can inhibit such interactions...
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PDB2Vec: Using 3D Structural Information for Improved Protein Analysis
In recent years, machine learning methods have shown remarkable results in various protein analysis tasks, including protein classification, folding...
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Learning protein fitness models from evolutionary and assay-labeled data
Machine learning-based models of protein fitness typically learn from either unlabeled, evolutionarily related sequences or variant sequences with...
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FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe
Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose...
