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The role of structural bioinformatics resources in the era of integrative structural biology

Aleksandras Gutmanas, Thomas J. Oldfield, Ardan Patwardhan, Sanchayita Sen, Sameer Velankar, Gerard J. Kleywegt
2013 Acta Crystallographica Section D: Biological Crystallography  
The history and the current state of the PDB and EMDB archives is briefly described, as well as some of the challenges that they face. It seems natural that the role of structural biology archives will change from being a pure repository of historic data into becoming an indispensable resource for the wider biomedical community. As part of this transformation, it will be necessary to validate the biomacromolecular structure data and ensure the highest possible quality for the archive holdings,
more » ... o combine structural data from different spatial scales into a unified resource and to integrate structural data with functional, genetic and taxonomic data as well as other information available in bioinformatics resources. Some recent developments and plans to address these challenges at PDBe are presented.
doi:10.1107/s0907444913001157 pmid:23633580 pmcid:PMC3640467 fatcat:d6szw6muxfgsrdunvsz4r4iovy

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank

Shuchismita Dutta, Dimitris Dimitropoulos, Zukang Feng, Irina Persikova, Sanchayita Sen, Chenghua Shao, John Westbrook, Jasmine Young, Marina A. Zhuravleva, Gerard J. Kleywegt, Helen M. Berman
2014 Biopolymers  
With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation. The Worldwide PDB (wwPDB) partners have periodically updated various aspects of structural data representation to improve the integrity and consistency of the archive. The remediation effort described here was focused on improving the representation of peptidelike inhibitor and antibiotic molecules so that they can be easily
more » ... fied and analyzed. Peptide-like inhibi-tors or antibiotics were identified in over 1000 PDB entries, systematically reviewed and represented either as peptides with polymer sequence or as single components. For the majority of the single-component molecules, their peptide-like composition was captured in a new representation, called the subcomponent sequence. A novel concept called "group" was developed for representing complex peptide-like antibiotics and inhibitors that are composed of multiple polymer and nonpolymer components. In addition, a reference dictionary was developed with detailed information about these peptide-like molecules to aid in their annotation, identification and analysis. Based on the experience gained in this remediation, guidelines, procedures, and tools were developed to annotate new depositions containing peptide-like inhibitors and antibiotics accurately and consistently.
doi:10.1002/bip.22434 pmid:24173824 pmcid:PMC3992913 fatcat:fsy4z23qcfgnvjj2jpn3stgwta

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Saqib Mir, Younes Alhroub, Stephen Anyango, David R Armstrong, John M Berrisford, Alice R Clark, Matthew J Conroy, Jose M Dana, Mandar Deshpande, Deepti Gupta, Aleksandras Gutmanas, Pauline Haslam (+10 others)
2017 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of
more » ... res solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.
doi:10.1093/nar/gkx1070 pmid:29126160 pmcid:PMC5753225 fatcat:j6ocp5cauvau3d7jd4gw3htwiq

PDBe: Protein Data Bank in Europe

Aleksandras Gutmanas, Younes Alhroub, Gary M. Battle, John M. Berrisford, Estelle Bochet, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Swanand P. Gore, Pauline Haslam, Rowan Hatherley (+15 others)
2013 Nucleic Acids Research  
The Protein Data Bank in Europe (pdbe.org) is a founding member of the Worldwide PDB consortium (wwPDB; wwpdb.org) and as such is actively engaged in the deposition, annotation, remediation and dissemination of macromolecular structure data through the single global archive for such data, the PDB. Similarly, PDBe is a member of the EMDataBank organisation (emdatabank.org), which manages the EMDB archive for electron microscopy data. PDBe also develops tools that help the biomedical science
more » ... nity to make effective use of the data in the PDB and EMDB for their research. Here we describe new or improved services, including updated SIFTS mappings to other bioinformatics resources, a new browser for the PDB archive based on Gene Ontology (GO) annotation, updates to the analysis of Nuclear Magnetic Resonance-derived structures, redesigned search and browse interfaces, and new or updated visualisation and validation tools for EMDB entries.
doi:10.1093/nar/gkt1180 pmid:24288376 pmcid:PMC3965016 fatcat:rv2cpebl5ffzbdppo654oahfly

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

Sameer Velankar, Glen van Ginkel, Younes Alhroub, Gary M. Battle, John M. Berrisford, Matthew J. Conroy, Jose M. Dana, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, Ingvar Lagerstedt (+21 others)
2015 Nucleic Acids Research  
The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite
more » ... or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and upto-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and sup-port expert users in analysing macromolecular structure data.
doi:10.1093/nar/gkv1047 pmid:26476444 pmcid:PMC4702783 fatcat:sqjtb2p3drbjncdycqrfr3m2lm

Crossing the Threshold: Women in Colonial City Space Sanchayita Paul Chakraborty Ghar Hote Angina Bidesh 1 : Women's Negotiation with the City in Colonial Bengal

Chandramukhi Bose, Kamini Sen, Kumudini Khastagir, Sarala Devi
2017 Sanglap   unpublished
The former members of the Bamahitaishani Sabha, Radharani Lahiri, Swarnaprova Bose, Kailashkamini Dutta, Swaraswati Sen, Kamini Sen, Kadambini Bose were the founding members of the Banga Mahila Samaj.  ...  Thus space had to be created for professional women in the workplace with the appointments of women teachers like the women medics like Kadambini Ganguly and Jamini Sen.  ...  © Sanchayita Paul Chakraborty, 2017.  ... 
fatcat:b4cnhcbnnvhddjdvvla6q7hug4

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Jasmine Y. Young, John D. Westbrook, Zukang Feng, Raul Sala, Ezra Peisach, Thomas J. Oldfield, Sanchayita Sen, Aleksandras Gutmanas, David R. Armstrong, John M. Berrisford, Li Chen, Minyu Chen (+37 others)
2017 Structure  
OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB
more » ... tion sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.
doi:10.1016/j.str.2017.01.004 pmid:28190782 pmcid:PMC5360273 fatcat:okamctypwvdrxfomgjio4rsvma

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi (+39 others)
2018 Database: The Journal of Biological Databases and Curation  
Citation details: Young,J.Y., Westbrook,J.D., Feng,Z. et al. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The V C The Author(s) worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability,
more » ... ccessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a highquality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce

The Uneasy Gaze – Appearing for Interviews to get Married – An Empirical Investigation into the Pre-marital Arranged Marriage Negotiations in Urban Kolkata

Sucharita Sen, PhD Scholar, Victoria University of Wellington, New Zealand.
2021 Rupkatha Journal on Interdisciplinary Studies in Humanities  
In its institutional aspect, the family (Sen, 2005) and neighbourhood become the epitome of patriarchy.  ...  Thus, the authority of the family over its members is more intimate, irreplaceable and deemed vital in an individual's life (Sen, 2020) .  ... 
doi:10.21659/rupkatha.v13n2.33 fatcat:evscgywmsneybepxsagwkvzzxy

A Conversation with Pranab Kumar Sen

Malay Ghosh, Michael J. Schell
2008 Statistical Science  
Professor Sen is the founding co-editor of two international journals: Sequential Analysis and Statistics and Decisions.  ...  After teaching for three years at Calcutta University, 1961--1964, Professor Sen came to Berkeley as a Visiting Assistant Professor in 1964.  ...  In the midst of that, my reading the "Sanchayita" of Rabindra Nath Tagore completely changed my views. The more I read the more I was fascinated by the lyrical powers of this great poet of all times.  ... 
doi:10.1214/08-sts255 fatcat:bg56wny5xzaddn2dc44gyzjrb4

Implementing an X-ray validation pipeline for the Protein Data Bank

Swanand Gore, Sameer Velankar, Gerard J. Kleywegt
2012 Acta Crystallographica Section D: Biological Crystallography  
We further wish to thank our collaborators on the wwPDB Deposition and Annotation Project core team (Zukang Feng, Tom Oldfield, Martha Quesada, Sanchayita Sen, John Westbrook and Jasmine Young) as well  ... 
doi:10.1107/s0907444911050359 pmid:22505268 pmcid:PMC3322607 fatcat:ulcf2o5jl5gozll2zbfnyfmk7y