Aleksandras Gutmanas
A5017822534- Protein Structure and Dynamics
- Enzyme Structure and Function
- Advanced Proteomics Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Glycosylation and Glycoproteins Research
- RNA and protein synthesis mechanisms
- Ubiquitin and proteasome pathways
- Metabolomics and Mass Spectrometry Studies
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Machine Learning in Bioinformatics
- interferon and immune responses
- Microbial Metabolism and Applications
- RNA modifications and cancer
- NMR spectroscopy and applications
- Microbial Community Ecology and Physiology
- DNA and Nucleic Acid Chemistry
- Genetics, Bioinformatics, and Biomedical Research
- Viral Infectious Diseases and Gene Expression in Insects
- Cancer Research and Treatments
- Machine Learning in Materials Science
- Advanced Electron Microscopy Techniques and Applications
- Molecular spectroscopy and chirality
European Bioinformatics Institute
2010-2024
University of Toronto
2010-2014
Princess Margaret Cancer Centre
2014
Wellcome Trust
2010-2013
Ontario Institute for Cancer Research
2010-2012
Structural Genomics Consortium
2006-2010
University of Gothenburg
2002-2005
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...
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 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...
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...
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...
Abstract The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural functional annotations of macromolecular structure data, contained the (PDB). goal PDBe-KB two-fold: (i) to increase visibility reduce fragmentation contributed by specialist data resources, make these more findable, accessible, interoperable reusable (FAIR) (ii) place their...
Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems treating disease. Despite the deposition of over 215 000 macromolecular structures in Protein Data Bank advent AI-based structure prediction tools such as AlphaFold2, RoseTTAFold, ESMFold, static representations are typically produced, which fail to fully capture motion. Here, we discuss importance integrating experimental with computational clustering explore landscapes that manifest...
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments improvements at PDBe addressing three challenging areas: data enrichment, functional reusability. New features Web site are discussed, including a context dependent menu providing links to raw experimental improved presentation structures solved by hybrid methods. also summarizes...
This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).
Abstract The archiving and dissemination of protein nucleic acid structures as well their structural, functional biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields life sciences. Protein Data Bank Europe (PDBe; pdbe.org ) team develops maintains several databases web services address this fundamental need. From data a member Worldwide PDB consortium (wwPDB; wwpdb.org ), PDBe Knowledge Base (PDBe‐KB;...
The Protein Data Bank in Europe (PDBe; pdbe.org) is a partner the Worldwide PDB organization (wwPDB; wwpdb.org) and as such actively involved managing single global archive of biomacromolecular structure data, PDB. In addition, PDBe develops tools, services resources to make structure-related data more accessible biomedical community. Here we describe recently developed, extended or improved services, including an animated structure-presentation widget (PDBportfolio), graphically display...
The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved managing the international archive of biomacromolecular structure data as one partners Worldwide (wwPDB; wwpdb.org). PDBe also develops new tools to make structural more widely and easily available biomedical community. has developed a browser access analyze using classification systems that are familiar chemists biologists. web pages describe individual PDB entries have been enhanced through introduction plain-English...
The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. worldwide PDB (wwPDB) international collaboration that manages archive according to FAIR principles: Findability, Accessibility, Interoperability Reusability. wwPDB recently developed OneDep, a unified tool deposition, validation biocuration macromolecules. All data deposited undergo critical review by Biocurators. This article...
The PDBe aggregated API is an open-access and open-source RESTful that provides programmatic access to a wealth of macromolecular structural data their functional biophysical annotations through 80+ endpoints. powered by the graph database (https://pdbe.org/graph-schema), integrative knowledge can be used as discovery tool answer complex biological questions.The up-to-date database, which has weekly releases with latest from Protein Data Bank, integrated updated UniProt, Pfam, CATH, SCOP...