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Showing posts with the label tools and softwares

Effortless PDB ID Retrieval: Using MATLAB for Structural Biology Research

 % Define the PDB ID you want to download pdb_id = 'desired PDB ID'; % Replace with your desired PDB ID ,    % Construct the URL for the PDB file pdb_url = strcat('https://files.rcsb.org/download/', pdb_id, '.pdb'); % Specify the download location on your computer download_dir = 'path_to_save_directory'; % Replace with your desired download directory % Create the full path for the downloaded file download_path = fullfile(download_dir, strcat(pdb_id, '.pdb')); % Download the PDB file try     pdb_data = webread(pdb_url);          % Open the file in binary write mode     fid = fopen(download_path, 'wb');          % Write the PDB data as binary     fwrite(fid, pdb_data);          % Close the file     fclose(fid);          disp(['PDB file ', pdb_id, ' downloaded successfully to ', download_path]); catch     error(' Failed to ...

Connected Papers: Navigating the Web of Scientific Knowledge

 In the ever-expanding realm of scientific research, staying updated with the latest developments and understanding the interconnectedness of various studies is a formidable challenge. This is where "Connected Papers" steps in as a valuable tool for researchers and academics. This blog will delve into the functionalities and usefulness of Connected Papers in the world of scientific exploration. The Power of Visualizing Connections Connected Papers isn't just another academic search engine; it's a bridge between the isolated islands of scientific knowledge. It harnesses the power of visualization to present academic papers in an interconnected web, allowing researchers to see at a glance how different studies relate to one another. By simply entering the title of a paper, users are presented with a network of related research. This visualization provides a holistic view of a particular field of study, making it easier to spot trends and gaps in the research landscape. ...

List of Venn diagram tools for bioinformaticians

The current biomedical hegemony of mass analytical "omics" domains such as genomics, proteomics, and metabolomics has enabled the rapid generation of enormously complex data sets with frequently unwieldy quantities of data points. Venn analysis is frequently used as the initial filtering step for large, complex, and interrelated data corpora. Numerous Venn diagram applications are already accessible for free to aid in the straightforward visual interpretation of biological datasets. The accessible tools for plotting Venn diagrams, on the other hand, are unevenly scattered throughout the literature. Here, we present a guided list to such tools that might assist scientists/researchers/students in visualizing their gene lists and generating biological hypotheses using integrated knowledge from biological pathway and GO databases. Table 1:List of tools and their features S. no Tool/program Number of input data sets (maximum) Platform Functional information Number of citation 1 B...