Ardan Patwardhan
A5091912447- Advanced Electron Microscopy Techniques and Applications
- Enzyme Structure and Function
- Electron and X-Ray Spectroscopy Techniques
- Protein Structure and Dynamics
- Cell Image Analysis Techniques
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Advanced X-ray Imaging Techniques
- Advanced Fluorescence Microscopy Techniques
- Advanced Proteomics Techniques and Applications
- Scientific Computing and Data Management
- Radioactive element chemistry and processing
- Bioinformatics and Genomic Networks
- Force Microscopy Techniques and Applications
- DNA Repair Mechanisms
- Machine Learning in Healthcare
- DNA and Nucleic Acid Chemistry
- RNA and protein synthesis mechanisms
- Radioactive contamination and transfer
- Photoacoustic and Ultrasonic Imaging
- Nuclear Physics and Applications
- Time Series Analysis and Forecasting
- Single-cell and spatial transcriptomics
- Bacterial Genetics and Biotechnology
- RNA modifications and cancer
European Bioinformatics Institute
2016-2025
Deutsches Elektronen-Synchrotron DESY
2024
Children's Hospital of Philadelphia
2018
Wolters Kluwer Health
2018
Wellcome Trust
2010-2017
JDSU (United States)
2013-2015
Imperial College London
1999-2011
Karolinska Institutet
1997-1999
KTH Royal Institute of Technology
1994-1999
Bhabha Atomic Research Centre
1968-1997
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...
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...
Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides unified portal deposition, retrieval and analysis 3DEM density maps, atomic models associated metadata (emdatabank.org). We provide here an overview the rapidly growing data archives, which include maps EM Data Bank map-derived Protein Bank. In addition, we describe progress approaches...
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...
Abstract Public archiving in structural biology is well established with the Protein Data Bank (PDB; wwPDB.org) catering for atomic models and Electron Microscopy (EMDB; emdb-empiar.org) 3D reconstructions from cryo-EM experiments. Even before recent rapid growth cryo-EM, there was an expressed community need a public archive of image data experiments validation, software development, testing training. Concomitantly, proliferation imaging techniques cells, tissues organisms using volume EM...
Abstract This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess quality models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility results different software developers and users (3) compare performance metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate relatively high accuracy cryo-EM derived...
Volume electron microscopy (vEM) is a group of techniques that reveal the 3D ultrastructure cells and tissues through continuous depths at least 1 micrometer. A burgeoning grassroots community effort fast building profile revealing impact vEM technology in life sciences clinical research.
The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data the PDB EMDB archives enriches, integrates disseminates structural information a variety ways. PDBe website has been redesigned based on an analysis user requirements, now offers intuitive access to improved value-added information. Unique includes lists reviews research articles that cite or mention entries as well figures legends from full-text open-access publications...
The Protein Data Bank in Europe (pdbe.org) is a founding member of the Worldwide PDB consortium (wwPDB; wwpdb.org) and as such actively engaged deposition, annotation, remediation dissemination macromolecular structure data through single global archive for data, PDB. Similarly, PDBe EMDataBank organisation (emdatabank.org), which manages EMDB electron microscopy data. also develops tools that help biomedical science community to make effective use their research. Here we describe new or...
Public data archives are the backbone of modern biological and biomedical research. While for molecules structures well-established, resources imaging do not yet cover full range spatial temporal scales or application domains used by scientific community. In last few years, technical barriers to building such have been solved first examples outputs from public image resources, often through linkage existing molecular published. Using successes biomolecular as a guide, we present rationale...
The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has recently been established. aims of the project are threefold: to build a coherent cryoEM community which will provide support individual scientists and act as focal point liaising with other communities, practising in their use software finally developers producing disseminating robust user-friendly programs. is closely modelled on CCP4 macromolecular crystallography, areas common interest such model fitting,...
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...
Bacteria produce functional amyloid fibers called curli in a controlled, noncytotoxic manner. These extracellular fimbriae enable biofilm formation and promote pathogenicity. Understanding biogenesis is important for appreciating microbial lifestyles will offer clues as to how disease-associated human might be ameliorated. Proteins encoded by the specific genes (csgA-G) are required production. We have determined structure of CsgC derived first structural model outer-membrane subunit...
Recent technological advances, such as the introduction of direct electron detector, have transformed field cryo-EM and landscape molecular cellular structural biology. This study analyses these trends from vantage point Electron Microscopy Data Bank (EMDB), public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter total number (4431). Structures at better than 6 Å resolution now represent one fastest-growing categories,...
Recent developments in 3-dimensional electron microcopy (3D-EM) techniques and a concomitant drive to look at complex molecular structures, have led rapid increase the amount of volume data available for biomolecules. This creates demand better methods analyse data, including improved scores comparison, classification integration different resolutions. To this end, we developed evaluated set scoring functions that compare 3D-EM volumes. test our used benchmark alignments derived from...
ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, Reusable (FAIR) users worldwide. describes the specific set attributes metadata associated with macromolecular structures modeled solely methods provides an extensible representation deposition, archiving, public dissemination predicted three-dimensional (3D) models macromolecules. It extension Protein Data...