Explanipedia

R2DT: a comprehensive platform for visualizing RNA secondary structure Open

Holly McCann, Caeden D. Meade, Loren Dean Williams, Anton S. Petrov, Philip Z. Johnson , et al. · 2025

RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R…

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

Jennifer Fleming, Paulyna Magaña, Sreenath Nair, Maxim Tsenkov, Damian Bertoni , et al. · 2025

The AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/) has made significant strides in enhancing its utility and accessibility for the life science research community. The recent integration of AlphaMissense predictions en…

R2DT: a comprehensive platform for visualising RNA secondary structure Open

Holly McCann, Caeden D. Meade, Loren Dean Williams, Anton S. Petrov, Philip Z. Johnson , et al. · 2024

RNA secondary (2D) structure visualisation is an essential tool for understanding RNA function. R2DT is a software package designed to visualise RNA 2D structures in consistent, recognisable, and reproducible layouts. The latest release, R…

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit Open

Sebastian Bittrich, Adam Midlik, Mihály Váradi, Sameer Velankar, S.K. Burley , et al. · 2024

With the ever‐expanding toolkit of molecular viewers, the ability to visualize macromolecular structures has never been more accessible. Yet, the idiosyncratic technical intricacies across tools and the integration complexities associated …

Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies Open

Joseph I. J. Ellaway, Stephen Anyango, Sreenath Nair, Hossam A. Zaki, Nurul Nadzirin , et al. · 2024

Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems and treating disease. Despite the deposition of over 215 000 macromolecular structures in the Protein Data Bank and the advent of …

Harnessing the 3D‐Beacons Network: A Comprehensive Guide to Accessing and Displaying Protein Structure Data Open

Paulyna Magaña, Sreenath Nair, Mihály Váradi, Sameer Velankar · 2024

Recent advancements in protein structure determination and especially in protein structure prediction techniques have led to the availability of vast amounts of macromolecular structures. However, the accessibility and integration of these…

PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank Open

Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa , et al. · 2024

The Protein Data Bank (PDB) is the global repository for public-domain experimentally determined 3D biomolecular structural information. The archival nature of the PDB presents certain challenges pertaining to updating or adding associated…

Alphafold Protein Structure Database and 3d-Beacons: New Data and Capabilities Open

Jennifer Fleming, Paulyna Magaña, Sreenath Nair, Maxim Tsenkov, Damian Bertoni , et al. · 2024

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank Open

Ibrahim Roshan Kunnakkattu, Preeti Choudhary, Lukáš Pravda, Nurul Nadzirin, Oliver S. Smart , et al. · 2023

While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we present PDBe CCDUtils, a versatile …

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data Open

Sri Devan Appasamy, John M. Berrisford, Romana Gáborová, Sreenath Nair, Stephen Anyango , et al. · 2023

Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the globa…

PDBImages: a command-line tool for automated macromolecular structure visualization Open

Adam Midlik, Sreenath Nair, Stephen Anyango, Mandar Deshpande, David Sehnal , et al. · 2023

Summary PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to genera…

EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023 Open

Matthew Thakur, Annalisa Buniello, Cath Brooksbank, Kim T Gurwitz, Matthew D. Hall , et al. · 2023

The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of…

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

Mihály Váradi, Damian Bertoni, Paulyna Magaña, Urmila Paramval, Ivanna Pidruchna , et al. · 2023

The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expanding from the initial 300k structur…

PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins Open

Hamidreza Ghafouri, Tamás Lázár, Alessio Del Conte, Luiggi G Tenorio Ku, Maria Cristina Aspromonte , et al. · 2023

The Protein Ensemble Database (PED) (URL: https://proteinensemble.org) is the primary resource for depositing structural ensembles of intrinsically disordered proteins. This updated version of PED reflects advancements in the field, denoti…

PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank Open

Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa , et al. · 2023

The Protein Data Bank (PDB) archive is the global repository for public-domain 3D biomolecular structural information. The archival nature of the PDB presents certain challenges pertaining to updating or adding associated annotations from …

The Protein Data Bank ( <span>PDB</span> ) and Macromolecular Structure Data Supporting Computer‐Aided Drug Design Open

David Armstrong, John M. Berrisford, Preeti Choudhary, Lukáš Pravda, James Tolchard , et al. · 2023

The Protein Data Bank (PDB) archives structural models of biological macromolecules, derived from experimental data. The PDB archive contains over 200,000 structures of proteins, DNA, RNA, and their complexes with small molecules, includin…

Challenges in bridging the gap between protein structure prediction and functional interpretation Open

Mihály Váradi, Maxim Tsenkov, Sameer Velankar · 2023

The rapid evolution of protein structure prediction tools has significantly broadened access to protein structural data. Although predicted structure models have the potential to accelerate and impact fundamental and translational research…

Clustering predicted structures at the scale of the known protein universe Open

Inigo Barrio‐Hernandez, Jingi Yeo, Jürgen Jänes, Milot Mirdita, Cameron L. M. Gilchrist , et al. · 2023

Proteins are key to all cellular processes and their structure is important in understanding their function and evolution. Sequence-based predictions of protein structures have increased in accuracy 1 , and over 214 million predicted struc…

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank Open

Ibrahim Roshan Kunnakkattu, Preeti Choudhary, Lukáš Pravda, Nurul Nadzirin, Oliver S. Smart , et al. · 2023

While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we present PDBe CCDUtils, a versatile …

PDBImages: A Command Line Tool for Automated Macromolecular Structure Visualization Open

Adam Midlik, Sreenath Nair, Stephen Anyango, Mandar Deshpande, David Sehnal , et al. · 2023

Summary: PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to gener…

Automated Pipeline for Comparing Protein Conformational States in the PDB to AlphaFold2 Predictions Open

Joseph I. J. Ellaway, Stephen Anyango, Sreenath Nair, Hossam A. Zaki, Nurul Nadzirin , et al. · 2023

Proteins, as molecular machines, are necessarily dynamic macromolecules that carry out essential cellular functions. Recognising their stable conformations is important for understanding the molecular mechanisms of disease. While AI-based …

Challenges in Bridging the Gap Between Protein Structure Prediction and Functional Interpretation Open

Mihály Váradi, Maxim Tsenkov, Sameer Velankar · 2023

The rapid evolution of protein structure prediction tools has significantly broadened access to protein structural data. Although predicted structure models have the potential to accelerate and impact fundamental and translational research…

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data Open

Sri Devan Appasamy, John M. Berrisford, Romana Gáborová, Sreenath Nair, Stephen Anyango , et al. · 2023

Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the globa…

Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data Open

Preeti Choudhary, Stephen Anyango, John M. Berrisford, James Tolchard, Mihály Váradi , et al. · 2023

More than 61,000 proteins have up-to-date correspondence between their amino acid sequence (UniProtKB) and their 3D structures (PDB), enabled by the Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource. SIFTS incorp…

Clustering predicted structures at the scale of the known protein universe Open

Martin Steinegger, Pedro Beltrão, Sameer Velankar, Mihály Váradi, Tanita Wein , et al. · 2023

Proteins are key to all cellular processes and their structure is important in understanding their function and evolution. Sequence-based predictions of protein structures have increased in accuracy with over 214 million predicted structur…

Clustering predicted structures at the scale of the known protein universe Open

Inigo Barrio‐Hernandez, Jingi Yeo, Jürgen Jänes, Tanita Wein, Mihály Váradi , et al. · 2023

Proteins are key to all cellular processes and their structure is important in understanding their function and evolution. Sequence-based predictions of protein structures have increased in accuracy with over 214 million predicted structur…

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models Open

Brinda Vallat, Gerardo Tauriello, Stefan Bienert, Juergen Haas, Benjamin Webb , et al. · 2023

The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors Open

Mihály Váradi, Nicola Bordin, Christine Orengo, Sameer Velankar · 2023

The function of proteins can often be inferred from their three-dimensional structures. Experimental structural biologists spent decades studying these structures, but the accelerated pace of protein sequencing continuously increases the g…

ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models Open

Brinda Vallat, Gerardo Tauriello, Stefan Bienert, Juergen Haas, Benjamin Webb , et al. · 2022

ModelCIF ( github.com/ihmwg/ModelCIF ) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable , and Reusable ( FAIR ) data to users worldwide. It i…

The impact of AlphaFold Protein Structure Database on the fields of life sciences Open

Mihály Váradi, Sameer Velankar · 2022

Arguably, 2020 was the year of high‐accuracy protein structure predictions, with AlphaFold 2.0 achieving previously unseen accuracy in the Critical Assessment of Protein Structure Prediction (CASP). In 2021, DeepMind and EMBL‐EBI developed…

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