By cataloging gene variation in peroxisome assembly diseases
we hope to accelerate the analysis of these variations
and understand their role in health and disease.
Database of DNA-Binding Proteins:
A comprehensive repository that catalogs DNA-binding proteins from various organisms. The database typically includes information about the protein's structure, function, and the specific DNA sequences or motifs they interact with.
Entries might include data derived from experimental studies, computational predictions, or a combination of both.
Data Submission and Sharing:
Researchers can submit their findings on DNA-binding proteins to the platform, contributing to a growing body of knowledge that is accessible to the scientific community.
The platform may support various data formats, including sequence data, structural models, and experimental annotations
Analytical Tools and Resources:
Prediction Tools: Computational tools for predicting DNA-binding domains in proteins, identifying potential DNA-binding sites, and modeling protein-DNA interactions.
Visualization Tools: Features for visualizing protein-DNA complexes, allowing researchers to explore the structural details of these interactions in 3D.
Sequence Alignment and Analysis: Tools for comparing DNA-binding proteins across different species, identifying conserved motifs, and analyzing evolutionary relationships.
Research and Publications:
Access to a collection of research papers, reviews, and case studies focused on DNA-binding proteins. This may include articles on the discovery of new DBPs, studies on their role in various cellular processes, and advances in the technology used to study them.
The platform might also highlight key publications that have utilized data, demonstrating the impact and relevance of the resource in scientific research.
Collaboration and Community:
A platform for connecting researchers working on DNA-binding proteins, facilitating collaboration, data sharing, and the exchange of ideas.
Forums or discussion groups where users can ask questions, share insights, and discuss recent developments in the field of DNA-binding proteins.
Educational Resources:
Tutorials, webinars, and guides on using the database and associated tools, as well as educational content on DNA-binding proteins, their functions, and methods for studying them.
Resources designed to support both novice researchers and experienced scientists in making the most of the platform's offerings.
Application Areas:
The data and tools available on DBPEx.g are relevant to a wide range of biological and medical research areas, including gene regulation, epigenetics, cancer research, and the development of novel therapeutics targeting DNA-protein interactions.
Use Cases:
Basic Research: Scientists studying the fundamental biology of DNA-binding proteins, their roles in gene expression, and their impact on cellular processes.
Drug Discovery: Researchers looking for potential targets in DNA-binding proteins for developing new drugs, especially in areas like oncology or infectious diseases.
Bioinformatics: Computational biologists who need access to datasets and tools for modeling protein-DNA interactions and predicting DNA-binding sites.
LOVD stands for Leiden Open (source) Variation Database. LOVD is designed to provide a flexible, freely available tool for gene-centered collection and display of DNA variations.
LOVD was developed approaching the "LSDB-in-a-Box" idea for the easy creation and maintenance of a fully web-based gene sequence variation database, that is platform-independent and uses PHP and MySQL open source software only. The basic gene-centered and modular design of the database follows the recommendations of the Human Genome Variation Society (HGVS) and focuses on the collection and display of the DNA sequence variations but it is extendable with clinical data with minimal effort. The open LOVD set up also facilitates functional extensions with scripts written by the community.
The development of (then nameless) LOVD started in late 2002, while it was first officially released in January, 2004. Before that LOVD was only in use by the Leiden Muscular Dystrophy pages, as a not-so-modular system with lots of characteristics specific for that website only. With the official release of LOVD in 2004 the system had become much more dynamic and customizing LOVD was made easy mostly by editing text-files.
In 2004, LOVD became available under the open source license GPL and with the 1.1.0 release most of the text-files had been replaced by online forms so customisations can be performed through the web interface. Early in 2005 the LOVD article was published, and in 2005 the development of LOVD was more targeted at improving the ease of use of the system.
In 2006 the development of LOVD 2.0 started after the decision was made to rewrite all of LOVD from scratch to be able to include a long list of upgrade suggestions that were hard to implement in LOVD 1.1.0. Aimed at modularity and data redundancy, LOVD 2.0 was meant to be a more flexible and more powerful successor of the popular 1.1.0 version and soon it received the interest of LOVD users eager to try out the all-new version.
LOVD 2.0 reached alpha stage in November 2006 after which a select group of enthusiastic LOVD users started testing the database software. With more features being added and bugs fixed rapidly, LOVD 2.0 reached beta stage in April 2007, after which more and more users started to upgrade their 1.1.0 databases to 2.0. Finally, in October 2007 LOVD 2.0 reached the stable stage but even now LOVD 2.0 is continuously improved. Every last Friday of the month, a new release is available from the LOVD website.