Sameer Velankar
A5042460017- Enzyme Structure and Function
- Protein Structure and Dynamics
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Advanced Proteomics Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Computational Drug Discovery Methods
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Advanced Electron Microscopy Techniques and Applications
- Glycosylation and Glycoproteins Research
- Mass Spectrometry Techniques and Applications
- Biotin and Related Studies
- DNA and Nucleic Acid Chemistry
- Cell Image Analysis Techniques
- Metabolomics and Mass Spectrometry Studies
- Machine Learning in Materials Science
- Research Data Management Practices
- Cancer Research and Treatments
- Semantic Web and Ontologies
- COVID-19 Clinical Research Studies
- Microbial Natural Products and Biosynthesis
European Bioinformatics Institute
2016-2025
Wellcome Trust
2011-2024
Worldwide Protein Data Bank
2012-2024
Milton Keynes Hospital NHS Foundation Trust
2024
Rutgers, The State University of New Jersey
2007-2014
Florida State University
2013
University of Cape Town
2013
Max Planck Institute for Biology of Ageing
2013
Centre National de la Recherche Scientifique
2013
Université Claude Bernard Lyon 1
2013
The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by v2.0 DeepMind, it has enabled unprecedented expansion the structural coverage known protein-sequence space. DB provides programmatic access to and interactive visualization predicted atomic coordinates, per-residue pairwise model-confidence estimates aligned errors. initial release contains over 360,000...
Abstract Protein structures can provide invaluable information, both for reasoning about biological processes and enabling interventions such as structure-based drug development or targeted mutagenesis. After decades of effort, 17% the total residues in human protein sequences are covered by an experimentally determined structure 1 . Here we markedly expand structural coverage proteome applying state-of-the-art machine learning method, AlphaFold 2 , at a scale that covers almost entire...
The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data biological macromolecules. Since 2003, PDB has been managed by Worldwide (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination 3D macromolecular data. Core Archive houses atomic coordinates more than 144 000 structural models proteins, DNA/RNA, their complexes with metals small...
Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) producing structural models of huge macromolecular machines assemblies, sometimes containing 100s millions non-hydrogen atoms. The performance requirements for visualization analysis tools delivering these data increasing rapidly. Significant progress in developing online,...
The AlphaFold Database Protein Structure (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 structures released in 2021. Enabled groundbreaking AlphaFold2 artificial intelligence (AI) system, predictions archived DB have been integrated into primary data resources such as PDB, UniProt, Ensembl, InterPro and MobiDB. Our manuscript details subsequent enhancements...
Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of cell. Recent developments in computational methods for protein structure predictions have reached accuracy experimentally determined models. Although this has been independently verified, implementation these across structural-biology applications remains to be tested. Here, we evaluate use AlphaFold2 (AF2) study characteristic structural elements; impact missense variants;...
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with mission to develop, test, distribute and promote software for macromolecular crystallography. CCP suite multiplatform collection of programs brought together by familiar execution routines, set common libraries graphical interfaces. has experienced several considerable changes since its last reference article, involving new infrastructure, original This which intended as general literature citation...
The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide partners to enhance the quality and consistency of international archive bio-macromolecular structure data, (PDB). PDBe also works closely collaborators at European Bioinformatics Institute scientific community around world databases services by adding curated maintained derived data existing structural PDB. We have developed a new database infrastructure based on remediated PDB...
The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) UniProt. two teams have developed semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, all protein chains PDB entries present database. This carried out every weekly release stored SIFTS includes cross-references other biological resources such as Pfam, SCOP, CATH, GO,...
Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort the Protein Data Bank in Europe (PDBe), Research Collaboratory for Structural Bioinformatics (RCSB) National Center Macromolecular Imaging (NCMI), is global 'one-stop shop' resource deposition retrieval cryoEM maps, models associated metadata. The unifies public access two major archives containing EM-based...
The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, reports for three-dimensional structures biological macromolecules are produced. These based on recommendations expert task forces representing crystallography, nuclear magnetic resonance, cryoelectron microscopy communities. provide useful metrics with which depositors can evaluate the quality experimental data, structural model, fit between them. module...
The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts/) was established in 2002 continues to operate as a collaboration between the Protein Data Bank Europe (PDBe; http://pdbe.org) UniProt Knowledgebase (UniProtKB; http://uniprot.org). is instrumental transfer of annotations protein structure sequence resources through provision up-to-date residue-level mappings entries from PDB UniProtKB. SIFTS also incorporates other biological resources,...
ABSTRACT We present the sixth report evaluating performance of methods for predicting atomic resolution structures protein complexes offered as targets to community‐wide initiative on Critical Assessment Predicted Interactions (CAPRI). The evaluation is based a total 20,670 predicted models 8 protein–peptide complexes, novel category in CAPRI, and 12 protein–protein CAPRI prediction Rounds held during years 2013‐2016. For two targets, focus was side‐chain conformation positions interfacial...
Abstract The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide (wwPDB), actively participates deposition, curation, validation, archiving and dissemination macromolecular structure data. PDBe supports diverse research communities their use structures by enriching PDB data providing advanced tools services for effective access, visualization analysis. This paper details enrichment at PDBe, including mapping RNA to Rfam, identification molecules that act as cofactors. has...
Proteins are key to all cellular processes and their structure is important in understanding function evolution. Sequence-based predictions of protein structures have increased accuracy1, over 214 million predicted available the AlphaFold database2. However, studying at this scale requires highly efficient methods. Here, we developed a structural-alignment-based clustering algorithm-Foldseek cluster-that can cluster hundreds millions structures. Using method, clustered database, identifying...
Abstract Deep-learning (DL) methods like DeepMind’s AlphaFold2 (AF2) have led to substantial improvements in protein structure prediction. We analyse confident AF2 models from 21 model organisms using a new classification protocol (CATH-Assign) which exploits novel DL for structural comparison and classification. Of ~370,000 models, 92% can be assigned 3253 superfamilies our CATH domain superfamily The remaining cluster into 2367 putative superfamilies. Detailed manual analysis on 618 of...
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with focus on single-particle analysis. The meeting attended by 45 experts in processing, model building refinement, validation, archiving such structures. This report describes the workshop's motivation history, topics discussed, consensus recommendations resulting from workshop. Some challenges future methods-development efforts this area are also...
UniChem is a freely available compound identifier mapping service on the internet, designed to optimize efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based resources. In past, creation maintenance of such links at EMBL-EBI, where several resources exist, has required independent efforts by each separate teams. These were complicated different data models, release schedules, differing business rules for normalization nomenclature that exist...
Abstract Summary: The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. CCD contains detailed descriptions for standard modified amino acids/nucleotides, ligands solvent molecules. Each definition includes of properties such as stereochemical assignments, descriptors, systematic names idealized coordinates. content, preparation, validation distribution this dataset are...