Sameer S Velankar

PDBe-SIFTS improves residue-level sequence-structure mapping with faster search, better scoring, and accurate alignment, comparable to expert curation.

The paper predicts quaternary structures of viral proteins using AlphaFold2 and AlphaFold-Multimer, identifying new insights into vaccinology and protease targets.

A parallelized BindCraft pipeline generated 306,146 in silico binder candidates against 8,296 human proteins, each with sequence, predicted complex and confidence metrics, freely accessible online.

The paper expands the AlphaFold Protein Structure Database to include proteome-scale quaternary structures, predicting 1.81M high-confidence protein complexes and revealing conserved structural clusters across domains of life.

This study introduces ECIFP, a method to analyze ligand binding modes in the PDB, showing it can identify similar binding sites and detect binding-mode similarities across diverse ligands.

RNAcentral integrates literature and gene-level data to enhance non-coding RNA sequence analysis and functional understanding.

The paper introduces a tool that links protein residue mentions in text to their corresponding positions in protein structures, enabling integrated exploration with experimental evidence.

FunCLAN categorises protein complex conformations, measures their similarities, and solves the chain equivalence problem using sequence similarity and superposition transformations.

The paper introduces PDBe tools for analysing small molecules in the PDB, enhancing ligand data access, interaction analysis, and functional role identification.

R2DT is a software platform for visualizing RNA secondary structures with enhanced features like SNP display and template-free visualization.

The paper develops a standardized system for validating biomolecular structures against NMR restraints using NEF and NMR-STAR formats, implemented in the wwPDB OneDep system.

The paper presents a human-in-the-loop system for identifying residue-level functional annotations from literature, achieving high precision, recall, and F1-measure.

The PDB NextGen Archive centralizes and streamlines access to integrated structural annotations and enriched data from wwPDB partners and external sources.

PDBe CCDUtils processes and analyzes small molecules from the PDB using RDKit, offering tools for property computation and database cross-references.

The paper standardizes naming and annotations for macromolecular complexes in the PDB using external resources, improving FAIRness and enabling better research and education.

The paper provides an overview of the EMDB archive, its current holdings, recent updates, and future plans.

A Foldseek-based linear-time structural clustering groups 52 million AlphaFold DB representatives into 2.27 million non-singleton clusters; 31% lack known structural or domain annotation.

The paper clusters experimentally determined protein structures to identify conformational states and compares them to AlphaFold2 predictions.

ModelCIF extends the PDBx/mmCIF standard to represent predicted 3D protein models, enabling FAIR data sharing for computational structural biology.

The paper uses AlphaFold2 to analyze protein structures from 21 organisms, identifying 26 novel superfamilies and expanding structural diversity insights.

The paper integrates up-to-date residue-level annotations from multiple databases into PDBx/mmCIF files to improve data interoperability and standardization.

PDB ProtVista is a sequence feature viewer that provides 2D visualization of residue-level annotations and integrates with 3D molecular viewers.

The paper predicts structures of disease-associated proteins without known structures, identifies functional sites, and explains 80% of mutations based on their proximity to these sites or structural impact.

3D-Beacons provides a federated network to unify access to protein structure data from multiple sources, enabling comparative analysis of models.

The paper assesses the value and sustainability of ELIXIR Core Data Resources, showing their critical role in preserving biological data and highlighting funding challenges.