12 hasil

AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities

Jennifer Fleming; Paulyna Magaña; Sreenath Sasidharan Nair dkk.

Journal of Molecular Biology · 2025 · Inggris · OpenAlex Scopus

• AlphaMissense scores now integrated, enabling large-scale pathogenicity analysis of protein missense variants. • Foldseek added for rapid, accurate protein structure searches and comparisons. • Bulk data downloads introduced for enhanced analysis and workflow integration. • 3D-Beacons updates…

EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools

Nils Oberg; Rémi Zallot; J.A. Gerlt

Journal of Molecular Biology · 2023 · Inggris · OpenAlex Scopus

The AlphaFold Database of Protein Structures: A Biologist’s Guide

Alessia David; Suhail A. Islam; Evgeny Tankhilevich dkk.

Journal of Molecular Biology · 2021 · Inggris · OpenAlex Scopus

AlphaFold, the deep learning algorithm developed by DeepMind, recently released the three-dimensional models of the whole human proteome to the scientific community. Here we discuss the advantages, limitations and the still unsolved challenges of the AlphaFold models from the perspective of a…

AlphaFold and Implications for Intrinsically Disordered Proteins

Kiersten M. Ruff; Rohit V. Pappu

Journal of Molecular Biology · 2021 · Inggris · OpenAlex Scopus

Accurate predictions of the three-dimensional structures of proteins from their amino acid sequences have come of age. AlphaFold, a deep learning-based approach to protein structure prediction, shows remarkable success in independent assessments of prediction accuracy. A significant epoch in…

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

Andrew I. Jewett; David Stelter; Jason Lambert dkk.

Journal of Molecular Biology · 2021 · Inggris · OpenAlex Scopus

Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop

Javier A. Jaimes; Nicole M. André; Joshua S. Chappie dkk.

Journal of Molecular Biology · 2020 · Inggris · OpenAlex Scopus

Structural insights into SARS-CoV-2 proteins

Rimanshee Arya; Shweta Kumari; Bharati Pandey dkk.

Journal of Molecular Biology · 2020 · Inggris · OpenAlex Scopus

Autophagy in Parkinson's Disease

Xu Hou; Jens O. Watzlawik; Fabienne C. Fiesel dkk.

Journal of Molecular Biology · 2020 · Inggris · OpenAlex Scopus

Impaired protein homeostasis and accumulation of damaged or abnormally modified protein are common disease mechanisms in many neurodegenerative disorders, including Parkinson's disease (PD). As one of the major degradation pathways, autophagy plays a pivotal role in maintaining effective turnover…

Liquid–Liquid Phase Separation and Its Mechanistic Role in Pathological Protein Aggregation

W. Michael Babinchak; Witold K. Surewicz

Journal of Molecular Biology · 2020 · Inggris · OpenAlex Scopus

FunRich enables enrichment analysis of OMICs datasets

Pamali Fonseka; Mohashin Pathan; Sai V. Chitti dkk.

Journal of Molecular Biology · 2020 · Inggris · OpenAlex Scopus

Mutations Strengthened SARS-CoV-2 Infectivity

Jiahui Chen; Rui Wang; Menglun Wang dkk.

Journal of Molecular Biology · 2020 · Inggris · OpenAlex Scopus

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive

Yana Rose; José M. Duarte; Robert Lowe dkk.

Journal of Molecular Biology · 2020 · Inggris · OpenAlex Scopus

The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves many millions of unique users worldwide by delivering experimentally-determined 3D structures of biomolecules integrated with >40 external data resources via RCSB.org, application programming interfaces…