Biomedical Scientist | PhD Candidate in Computational Modeling
Specialist in Computer-Aided Drug Design (CADD)
Bioinformatics, Molecular Modeling & AI

I am a biomedical scientist with 13+ years of experience in Computer-Aided Drug Design (CADD), focusing on molecular docking, receptor flexibility strategies, and structure-based drug discovery.

I work at the intersection of structural bioinformatics, transcriptomics, and artificial intelligence, translating biological complexity into computational strategies for drug discovery and data-driven research.

• Structure-Based Drug Design (SBDD)
• Molecular Docking (rigid and flexible receptor approaches)
• Receptor flexibility modeling
• Redocking and cross-docking validation
• Binding affinity prediction
• Structural modeling of proteins and variants (SNPs)
• Virtual screening strategies
• Benchmark development and validation

• RNA-Seq analysis and transcriptomics
• NGS data processing
• Large-scale biological dataset analysis
• Integration of structural and omics data
• Development of bioinformatics pipelines

• Machine Learning fundamentals
• AI applied to biological and educational contexts
• Data-driven modeling strategies

• Python (pandas, numpy, matplotlib, scikit-learn)
• Bash scripting
• C/C++
• Java
• Jupyter Notebook

• Molecular docking programs and platforms
• Structural modeling tools
• Basic experience in Molecular Dynamics and Normal Mode Analysis
• Linux/Bash environments
• Workflow automation
• Git & GitHub

• Large-scale RNA-Seq data retrieval and processing
• Download and curation of public NGS datasets
• Differential gene expression analysis
• Exploratory transcriptome analysis
• Integration of structural and omics data
• GWAS database construction and data organization
• Development of reproducible bioinformatics pipelines
• Docker

• Professor in Software Development and Artificial Intelligence programs
• Researcher in molecular modeling and CADD methodologies
• Supervisor of computational and data-driven projects
• Developer of interdisciplinary teaching materials in AI and bioinformatics

• Ph.D. Research: Advancing receptor flexibility modeling in molecular docking using the DockThor platform
• Bioinformatics & Transcriptomics: Large-scale genomic and RNA-Seq data analysis; development of the Soybean Expression Atlas
• GWAS Data Integration: Construction and integration of a GWAS-ready dataset for Glycine max, combining phenotypic and genotypic data for agronomic traits
• Science Communication: Development of tutorials, workshops, and educational materials to make computational science more accessible
• Web Development: Development and maintenance of the Venâncio Research Group website using Hugo

• Lattes Curriculum • ORCID • ResearchGate • LinkedIn •

• Email: almk.karl@gmail.com

⭐ Open to collaborations in CADD, molecular modeling, structural bioinformatics, and interdisciplinary computational research.