Sameer Velankar
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View article: Linking protein residues in literature and structure
Linking protein residues in literature and structure Open
Protein structures are crucial in understanding function, mechanism and disease-causing variants of proteins within any living cell. A number of experimental techniques are employed by researchers to determine said structure. Through struc…
View article: RNAcentral in 2026: Genes and literature integration
RNAcentral in 2026: Genes and literature integration Open
RNAcentral was founded in 2014 to serve as a comprehensive database of non-coding RNA sequences. It began by providing a single unified interface to more specialised resources, and now contains 45 million sequences. It has grown beyond pro…
View article: Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities
Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities Open
Communities of experts collaborating on scientific or technical projects are drivers of innovation across the life sciences. The ELIXIR research infrastructure organises scientific- and technological-themed communities as one of its key me…
View article: Biomolecular Interaction Prediction in the Pre‐ and Post‐ <scp>AlphaFold</scp> Era: The 8th <scp>CAPRI</scp> Evaluation
Biomolecular Interaction Prediction in the Pre‐ and Post‐ <span>AlphaFold</span> Era: The 8th <span>CAPRI</span> Evaluation Open
We report on the 8th CAPRI Evaluation period, capturing the assessment of CAPRI Rounds 47 to 55 (excluding the CASP and COVID‐related Rounds), which have witnessed the transition to AI‐driven prediction tools such as AlphaFold and related …
View article: FunCLAN: A novel and generalisable method for categorising protein complex conformations, measuring their similarities, and solving the chain equivalence problem
FunCLAN: A novel and generalisable method for categorising protein complex conformations, measuring their similarities, and solving the chain equivalence problem Open
We present FunCLAN, a novel method for finding, categorising, and measuring conformational relationships between protein complexes, as well as for finding corresponding chain pairs between them. Its purpose is to provide a general tool, ap…
View article: Protein-protein interaction prediction in the pre- and post-AlphaFold era: the 8th CAPRI evaluation
Protein-protein interaction prediction in the pre- and post-AlphaFold era: the 8th CAPRI evaluation Open
We report on the 8th CAPRI Evaluation period, capturing the assessment of CAPRI Rounds 47 to 55 (excluding the CASP and COVID-related Rounds), which have witnessed the transition to AI-driven prediction tools such as AlphaFold and related …
View article: Updates to the CASP infrastructure in 2024
Updates to the CASP infrastructure in 2024 Open
View article: <scp>PDBe</scp> tools for an in‐depth analysis of small molecules in the Protein Data Bank
<span>PDBe</span> tools for an in‐depth analysis of small molecules in the Protein Data Bank Open
The Protein Data Bank (PDB) is the primary global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands, proteins, and nucleic acids. PDB contains over 47,000 unique small mole…
View article: AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities
AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities Open
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…
View article: PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures Open
Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional …
View article: PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank
PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank Open
The Protein Data Bank (PDB) is the primary global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands, proteins, and nucleic acids. PDB contains over 47,000 unique small mole…
View article: R2DT: a comprehensive platform for visualising RNA secondary structure
R2DT: a comprehensive platform for visualising RNA secondary structure Open
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…
View article: Dataset from a human-in-the-loop approach to identify functionally important protein residues from literature
Dataset from a human-in-the-loop approach to identify functionally important protein residues from literature Open
View article: Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit
Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit Open
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 …
View article: Innovative Packaging: Its Impact on Consumer Purchasing Decisions in the Food Sector.
Innovative Packaging: Its Impact on Consumer Purchasing Decisions in the Food Sector. Open
This study examines how consumers' decisions about what to buy in the food industry are influenced by creative packaging, with a focus on the importance of sustainability and design. The research investigates how packaging aesthetics and e…
View article: IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods Open
IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, a…
View article: Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank
Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank Open
Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards…
View article: Human-in-the-loop approach to identify functionally important residues of proteins from literature
Human-in-the-loop approach to identify functionally important residues of proteins from literature Open
We present a novel system that leverages curators in the loop to develop a dataset and model for detecting residue-level functional annotations and other protein structure features from standard publication text. Our approach involves the …
View article: Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank
Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank Open
Summary Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of s…
View article: PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank Open
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…
View article: EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023
EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023 Open
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…
View article: PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank
PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank Open
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 …
View article: The Protein Data Bank ( <scp>PDB</scp> ) and Macromolecular Structure Data Supporting Computer‐Aided Drug Design
The Protein Data Bank ( <span>PDB</span> ) and Macromolecular Structure Data Supporting Computer‐Aided Drug Design Open
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…
View article: Challenges in bridging the gap between protein structure prediction and functional interpretation
Challenges in bridging the gap between protein structure prediction and functional interpretation Open
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…
View article: Clustering predicted structures at the scale of the known protein universe
Clustering predicted structures at the scale of the known protein universe Open
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…
View article: Structural biology: The transformational era
Structural biology: The transformational era Open
Structural biology has been undergoing an unprecedented transformation recently thanks to major breakthroughs in experimental methods such as cryogenic electron microscopy (cryo-EM) and ground-breaking computational approaches for predicti…
View article: EOSC-Life Report on the work of the Open Call Projects
EOSC-Life Report on the work of the Open Call Projects Open
This Deliverable 3.3 is a report on the Digital Life Sciences Open Call and two Internal Calls organised by EOSC-Life WP3. The organisation of these Calls followed the successful integration and support of 8 Demonstrator projects which pro…
View article: PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank Open
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 …
View article: PDBImages: A Command Line Tool for Automated Macromolecular Structure Visualization
PDBImages: A Command Line Tool for Automated Macromolecular Structure Visualization Open
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…
View article: Automated Pipeline for Comparing Protein Conformational States in the PDB to AlphaFold2 Predictions
Automated Pipeline for Comparing Protein Conformational States in the PDB to AlphaFold2 Predictions Open
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 …