Results 61 to 70 of about 1,082 (162)

PDBe tools for an in‐depth analysis of small molecules in the Protein Data Bank

Protein Science, Volume 34, Issue 4, April 2025.
Abstract The Protein Data Bank (PDB) is the primary global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands, proteins, and nucleic acids. PDB contains over 47,000 unique small molecules bound to the macromolecules.
Preeti Choudhary, Ibrahim Roshan Kunnakkattu, Sreenath Nair, Dare Kayode Lawal, Ivanna Pidruchna, Marcelo Querino Lima Afonso, Jennifer R. Fleming, Sameer Velankar   +7 more
wiley   +1 more source

The Biocurator: Connecting and Enhancing Scientific Data

PLoS Computational Biology, 2006
From Impressionism and Pop Art to phosphorylation sites and interacting atom pairs, the realm of curation has been expanded. The recent growth of bioinformatics, driven by exponentially growing data, advanced computing techniques, and increased funding from private and governmental organizations, has created the need for novel strategies to adequately ...
Nima Salimi, Randi Vita
openaire   +4 more sources

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

Protein Science, Volume 34, Issue 4, April 2025.
Abstract The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three‐dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe ...
Sebastian Bittrich, Alexander S. Rose, David Sehnal, Jose M. Duarte, Yana Rose, Joan Segura, Dennis W. Piehl, Brinda Vallat, Chenghua Shao, Charmi Bhikadiya, Jesse Liang, Mark Ma, David S. Goodsell, Stephen K. Burley, Shuchismita Dutta   +14 more
wiley   +1 more source

A FAIR-Based Approach to Enhancing the Discovery and Re-Use of Transcriptomic Data Assets for Nuclear Receptor Signaling Pathways

Data Science Journal, 2017
Public transcriptomic assets in the nuclear receptor (NR) signaling field hold considerable collective potential for exposing underappreciated aspects of NR regulation of gene expression.
Scott A. Ochsner, Yolanda F. Darlington, Apollo McOwiti, Wasula H. Kankanamge, Alexey Naumov, Lauren B. Becnel, Neil J. McKenna   +6 more
doaj   +1 more source

BI‐LAVA: Biocuration With Hierarchical Image Labelling Through Active Learning and Visual Analytics

Computer Graphics Forum, Volume 44, Issue 1, February 2025.
BI‐LAVA is an innovative labeling system designed for the hierarchical annotation of image modalities in biocuration. By integrating visual analytics with machine learning techniques, BI‐LAVA facilitates the understanding of biomedical datasets for users with limited expertise.
Juan Trelles, Andrew Wentzel, William Berrios, Hagit Shatkay, G. Elisabeta Marai   +4 more
wiley   +1 more source

CardioTF, a database of deconstructing transcriptional circuits in the heart system [PDF]

PeerJ, 2016
Background: Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper ...
Yisong Zhen
doaj   +2 more sources

Mechanisms of action of monoclonal antibodies in oncology integrated in IMGT/mAb-DB

Frontiers in Immunology, 2023
BackgroundCancer cells activate different immune checkpoint (IC) pathways in order to evade immunosurveillance. Immunotherapies involving ICs either block or stimulate these pathways and enhance the efficiency of the immune system to recognize and attack
Taciana Manso, Anjana Kushwaha, Nika Abdollahi, Patrice Duroux, Véronique Giudicelli, Sofia Kossida   +5 more
doaj   +1 more source

Databases and bioinformatics tools for rice research

Current Plant Biology, 2016
Rice is one of the most important agricultural crop in the world and widely studied model plant. The completion of whole genome sequence of rice (Oryza sativa) and high-throughput experimental platforms have led to the generation of the tremendous amount
Priyanka Garg, Pankaj Jaiswal
doaj   +1 more source

Mapping the landscape of biocuration – where are the biocurators and what do they need?

, 2019
These slides were presented as part of a workshop on ‘Mapping the landscape of biocuration’ at the Biocuration 2019 conference. This work forms part of an ELIXIR Implementation Study. The slides are a summary of the preliminary analysis of a survey conducted by ELIXIR and the International Society of Biocuration which was designed to map the landscape ...
Holinski, Alexandra, Burke, Melissa, Morgan, Sarah, Palagi, Patricia, McQuilton, Peter   +4 more
openaire   +1 more source

TrialSieve: A Comprehensive Biomedical Information Extraction Framework for PICO, Meta-Analysis, and Drug Repurposing

Bioengineering
This work introduces TrialSieve, a novel framework for biomedical information extraction that enhances clinical meta-analysis and drug repurposing. By extending traditional PICO (Patient, Intervention, Comparison, Outcome) methodologies, TrialSieve ...
David Kartchner, Haydn Turner, Christophe Ye, Irfan Al-Hussaini, Batuhan Nursal, Albert J. B. Lee, Jennifer Deng, Courtney Curtis, Hannah Cho, Eva L. Duvaris, Coral Jackson, Catherine E. Shanks, Sarah Y. Tan, Selvi Ramalingam, Cassie S. Mitchell   +14 more
doaj   +1 more source