TKitOC PRO v8+: An Interactive Cloud-Based Platform Integrating Target Discovery and Chemoinformatics Workflows
- 1Laboratorio de Inmunología y Genética Facultad de Química
- 2UAEMéx Paseo Colón
Abstract
The transition from biological target identification to structure-based molecular analysis commonly requires researchers to combine multiple software environments, file formats, and external web services. This fragmentation can increase preprocessing effort and create practical barriers for computational biology education and early-stage in silico research. Here, we present TKitOC PRO v8+, an interactive cloud-based platform designed to integrate sequence analysis, molecular diagnostics, structural data preparation, and chemoinformatics workflows within a unified graphical interface deployed through Google Colab. The platform unifies the in silico workflow by distributing functionalities across 13 modular tabs organized into two core pipelines. The Target Discovery and Molecular Diagnostics pipeline provides nucleotide and protein sequence processing, open reading frame analysis across six frames, codonpreference back-translation, automated primer design through Primer3, in silico primer specificity assessment using NCBI BLASTn, and protein functional annotation via InterPro coupled with an immediate local motif-based Fast-Track algorithm. The Structure and Chemoinformatics pipeline integrates molecular descriptor calculation through RDKit, structural visualization with py3Dmol, ligand extraction and format preparation, and automated assembly of receptor–ligand complexes via DockPrime from externally generated docking outputs. As a proof-of-concept case study, we applied the platform to the KPC-2 carbapenemase—a critical antimicrobial resistance determinant from the ESKAPE group—using the crystallographic structure PDB 2OV5. The workflow started from the deposited protein sequence, verified taxonomic identity via BLASTn identified the Class Aβ-lactamase target, generated a corresponding nucleotide representation through back-translation, assessed sequence correspondence through BLASTn, generated candidate primer pairs targeting the blaKPC gene, and connected the resulting target characterization with functional annotation and structural analysis. The resulting workflow demonstrates how TKitOC PRO v8+ can reduce manual transitions between heterogeneous computational tools and provide an accessible environment for bioinformatics and chemoinformatics training and preliminary research workflows.
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BibTeX
@misc{navasaldivar2026tkitoc,
title = {{TKitOC PRO v8+: An Interactive Cloud-Based Platform Integrating Target Discovery and Chemoinformatics Workflows}},
author = {Angel Eduardo Nava-Saldivar and Jonnathan Guadalupe Santillán-Benítez},
howpublished = {ChemRxiv},
year = {2026},
month = sep,
doi = {10.26434/chemrxiv.15009662/v1},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009662/v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - TKitOC PRO v8+: An Interactive Cloud-Based Platform Integrating Target Discovery and Chemoinformatics Workflows
AU - Angel Eduardo Nava-Saldivar
AU - Jonnathan Guadalupe Santillán-Benítez
PY - 2026
DA - 2026/09/29
PB - ChemRxiv
DO - 10.26434/chemrxiv.15009662/v1
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009662/v1
AB - The transition from biological target identification to structure-based molecular analysis commonly requires researchers to combine multiple software environments, file formats, and external web services. This fragmentation can increase preprocessing effort and create practical barriers for computational biology education and early-stage in silico research. Here, we present TKitOC PRO v8+, an interactive cloud-based platform designed to integrate sequence analysis, molecular diagnostics, structural data preparation, and chemoinformatics workflows within a unified graphical interface deployed through Google Colab. The platform unifies the in silico workflow by distributing functionalities across 13 modular tabs organized into two core pipelines. The Target Discovery and Molecular Diagnostics pipeline provides nucleotide and protein sequence processing, open reading frame analysis across six frames, codonpreference back-translation, automated primer design through Primer3, in silico primer specificity assessment using NCBI BLASTn, and protein functional annotation via InterPro coupled with an immediate local motif-based Fast-Track algorithm. The Structure and Chemoinformatics pipeline integrates molecular descriptor calculation through RDKit, structural visualization with py3Dmol, ligand extraction and format preparation, and automated assembly of receptor–ligand complexes via DockPrime from externally generated docking outputs. As a proof-of-concept case study, we applied the platform to the KPC-2 carbapenemase—a critical antimicrobial resistance determinant from the ESKAPE group—using the crystallographic structure PDB 2OV5. The workflow started from the deposited protein sequence, verified taxonomic identity via BLASTn identified the Class Aβ-lactamase target, generated a corresponding nucleotide representation through back-translation, assessed sequence correspondence through BLASTn, generated candidate primer pairs targeting the blaKPC gene, and connected the resulting target characterization with functional annotation and structural analysis. The resulting workflow demonstrates how TKitOC PRO v8+ can reduce manual transitions between heterogeneous computational tools and provide an accessible environment for bioinformatics and chemoinformatics training and preliminary research workflows.
ER -