| Santi Garcia-Vallvé Biochemistry and Biotechnology Department Rovira i Virgili University. Tarragona. ORCID ID: 0000-0002-0348-7497 Contact address: |
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ACADEMIC RECORD
MERITS RELATED TO RESEARCH/ACADEMIC ACTIVITY
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| PhD STUDENTS |
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Bioinformatic Tools and Databases Developed |
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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 https://github.com/URV-cheminformatics/PDB-CAT https://chemrxiv.org/engage/chemrxiv/article-details/66b66b0bc9c6a5c07aa936de https://ariadnallopps-organization.gitbook.io/pdb-cat https://colab.research.google.com/github/URV-cheminformatics/PDB-CAT/blob/main/PDB-CAT-colab.ipynb |
| 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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Activity Cliffs Calculator |
| Compute activity Cliffs (pairs or groups of structurally similar compounds that are active against the same target but have large differences in potency) from an xls file containing a set of molecules. | |
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GC skew Plot Generation https://gcskew.runmercury.com/mercury/GCskew_mercury |
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This tool generates a GC skew and a cumulative GC skew plot from a fasta file containing the complete genome sequence of a bacterium. The GC skew plot can allow predicting the origin of replication of a genome from its sequence. |
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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) https://github.com/URVquimioinformatica-COS/VHELIBS Validation Helper for LIgands and Binding Sites (VHELIBS) - New version (July 2026) Author: Said Trujillo De León |
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Cereto-Massagué A, Ojeda MJ, Joosten RP, Valls C, Mulero M, Salvado MJ, Arola-Arnal A, Arola L, Garcia-Vallvé S, Pujadas G. (2013). The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. J Cheminform., 5(1):36. doi: 10.1186/1758-2946-5-36 |
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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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RCDI / eRCDI |
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The RCDI server is a web-application that calculates the Relative Codon Deoptimization Index (RCDI) and an expected value of the RCDI for a set of query sequences by generating random sequences with similar G+C content and amino acid composition to the input. This expected RCDI therefore provides a direct threshold value for discerning whether the differences in the RCDI value are statistically significant and arise from the codon preferences or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences. Please, click here to get a quick tutorial. |
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CAIcal/E-CAI http://genomes.urv.cat/CAIcal/ |
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Puigbo P, Bravo IG and Garcia-Vallve S. 2008 E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). BMC Bioinformatics, 9:65. |
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This server performs several computations in relation to codon usage and the codon adaptation of DNA or RNA sequences to host organisms. The E-CAI server is a web-application and an executable program that calculates the expected value of the Codon Adaptation Index (CAI) for a set of query sequences by generating random sequences with similar G+C content and amino acid composition to the input. This expected CAI therefore provides a direct threshold value for discerning whether the differences in the CAI value are statistically significant and arise from the codon preferences or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences. |
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Highly Expresse Genes Database |
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The HEG-DB is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage for all genes, and the analysis of their highly expressed genes. For each genome, the database contains functional and positional information about the predicted group of highly expressed genes. This information can also be accessed using a search engine. Among other statistical parameters, the database also provides the Codon Adaptation Index for all of the genes using the codon usage of the highly expressed genes as a reference set. The "Pathway Tools Omics Viewer" from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes. |
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OPTIMIZER http://genomes.urv.cat/OPTIMIZER/ http://ppuigbo.me/programs/optimizerlite/ https://usuaris.tinet.cat/debb/OPTIMIZE/ http://genomes.urv.cat/OPTIMIZER/Optimizer_from_protein.html |
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OPTIMIZER is an on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression level. Users can introduce their own preference tables to be used in the optimization process or use pre-computed tables from several prokaryotic species under a strong translational selection. Three methods of optimization are available: the 'one amino acid - one codon' approach, a random approach or an intermediate one. Several options, such as avoiding specific restriction sites and several outputs, are also available. This server can be useful for predicting and optimizing the level expression of a gene in heterologous gene expression. |
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TOPD/fMtS |
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TOPD/FMTS is a new software for comparing phylogenetic trees. It has been developed to calculate the differences between trees. The software implements several previously described methods and new algorithms for comparing phylogenetic trees. It combines the TOPD program (TOPological Distance), which compares two trees with the same taxa or two pruned trees, and the FMTS program (From Multiple To Single), which converts multi-gene family trees to single-gene trees. |
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Horizontal Gene Tranfer Database http://genomes.urv.cat/HGT-DB/ (not available anymore) https://usuaris.tinet.cat/debb/HGT/welcomeOLD.html (an old version) |
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The HGT-DB is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer. The current version of the database includes the analysis of 94 bacterial and archaeal complete genomes, including multiple chromosomes and strains, when available. Other complete genomes will be added progressively. |
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DendroUPGMA |
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S. Garcia-Vallve, J. Palau and A. Romeu (1999) Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Molecular Biology and Evolution 9:1125-1134. |
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Use this program to create a dendrogram from a set of variables. The program calculates a similarity coefficient between pairs of sets of variables, transforms these coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm. |
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| TRANSLATE |
Translate |
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A web server utility that translates a set of DNA sequences. |
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| REVIEWER OF THE FOLLOWING JOURNALS |
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RECENT TALKS:
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