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PLII-Atlas: Protein-Ligand Interaction Database
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| PLII-Atlas is a database of protein-ligand complexes derived from the PDB that integrates detailed intermolecular interaction data with experimentally determined binding affinity and activity measurements, such as Ki, Kd, and IC50 values. It provides advanced search capabilities, enables visualization of the interactions of individual complexes in both tabular and interactive 3D formats, and supports comparative analyses across distinct sets of protein-ligand complexes. | |
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pICkIT: Automated analysis of protein-ligand interactions
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| pICkIT is an open-source Python library for the extraction, filtering, and analysis of protein-ligand interaction data from large structural datasets. It was built to process the interaction files generated by tools such as Arpeggio, whose raw output is often too large and complex for manual inspection. pICkIT parses these files into a compact, structured interaction matrix and provides a modular API for filtering, summarizing, comparing, and visualizing interaction patterns across hundreds or thousands of protein-ligand complexes - turning hundreds of megabytes of raw JSON into a few kilobytes of publication-ready data, in seconds. | |
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PDB-CAT: Classification and Analysis Tool for PDBx/mmmCIF files
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Llop-Peiró A, Trujillo-De León S, Pujadas G, Garcia-Vallvé S, Gimeno A. PDB-CAT: A user-friendly tool to classify and analyze PDB protein-ligand complexes. Protein Sci. 2025 Dec;34(12):e70379. doi: 10.1002/pro.70379. PDB-CAT is a program that classifies a group of protein structures based on their ligands into three categories: apo, covalently, and non-covalently bonded. Besides this classification, the program can verify if there are any mutations in the protein sequence by comparing it to a reference sequence. PDB-CAT is designed to be user-friendly, with its output clearly defining every entity present in each entry to facilitate decision-making. |
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SARS-CoV-2 Mutation Portal
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Saldivar-Espinoza B, Garcia-Segura P, Novau-Ferré N, Macip G, Martínez R, Puigbò P, Cereto-Massagué A, Pujadas G, Garcia-Vallve S. The Mutational Landscape of SARS-CoV-2. Int J Mol Sci. 2023 May 22;24(10):9072. doi: 10.3390/ijms24109072 |
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| This database contains SARS-CoV-2 mutation data from the beginning of the COVID-19 pandemic. The data are derived from the analysis of more than 4.5 million complete genomes available in GISAID. Various information such as mutation type, location, % of times observed, countries, lineages, VOCs, ..... is collected. The results are displayed in tabular form and in a scatter plot. | |
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Validation Helper for LIgands and Binding Sites (VHELIBS)
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The Validation HElper for LIgands and Binding Sites (VHELIBS) aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e. users with little or no crystallography knowledge) by checking how their coordinates fit to their corresponding electron density map and letting the user to use models from either the PDB or PDB_REDO. The user can specify threshold values for a series of properties related with coordinates to electron density fitting (where Real Space R, Real Space Correlation Coefficient and average occupancy are the ones used by default) and, VHELIBS will automatically label residues and ligands with values within the specified limits, and the rest as either dubious or bad based on an user-configurable tolerance value. The user then is able to visually check the fitness quality of the residues/ligands to their corresponding electron density map, and reclassify them if needed. |
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DecoyFinder
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DecoyFinder is a graphical tool which helps finding sets of decoy molecules for a given group of active ligands. It does so by finding molecules which have a similar number of rotational bonds, hydrogen bond acceptors, hydrogen bond donors, logP value and molecular weight, but are chemically different, which is defined by a maximum Tanimoto value threshold between active ligand and decoy molecule MACCS fingerprints. Optionally, a maximum Tanimoto value threshold can be set between decoys in order to assure chemical diversity in the decoy set. |
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