CV

Contact Information

Name Yonglan Liu
Professional Title Computational Chemist | Computational Structural Biologist
Email liuyonglan04@gmail.com
Location 31 Center Dr, Bethesda, Maryland MD 20894

Professional Summary

Computational Chemist, Computational Structural Biologist, and AI Scientist with a hybrid background in machine learning, deep learning, and physics-based molecular modeling, molecular dynamics (MD) simulation for drug discovery, including protein/peptide and small molecules. I design and lead integrated physics- and ML-driven discovery platforms that connect molecular sequence and structure to functional and developability outcomes. Experienced in curating and governing large-scale chemical and biological datasets, building multimodal predictive and generative AI models, and partnering with experimental teams across medicinal chemistry, protein engineering, and structural biology to translate computational insight into concrete optimization hypotheses to guide synthesis and prioritization decisions across design–make–test–learn (DMTL) cycles.

Education

  • 2017 - 2021

    Akron, OH, USA

    PhD
    The University of Akrons
    Chemical Engineering
  • 2010 - 2014

    Chongqing, China

    BS
    Chongqing University
    Bioengineering

Experience

  • 2025 - present

    Bethesda, MD, US

    Senior Technical Analyst | Computational Chemist
    Guidehouse
    Senior Technical Analyst at Guidehouse and serving as a Computational Chemist at NIH, leverage different computational technicals for drug discovery.
    • Led the design and operationalization of integrated, end-to-end discovery workflows combining docking, MD-based refinement, alchemical free energy perturbation (FEP), and ML-driven developability prediction to guide compound prioritization across NIH-funded programs.
    • Owned the architecture and reproducibility standards for alchemical FEP pipelines using OpenMM and MBAR, enabling quantitative protein–ligand binding affinity prediction and decision support for structure-based lead optimization.
    • Curated and analyzed target-focused chemical libraries to support iterative design–test–learn cycles, partnering with medicinal chemists to leverage free-energy–informed SAR analysis for hypothesis refinement and compound selection.
    • Applied structure-based, ligand-based, and fragment-based design strategies to manage trade-offs among potency, selectivity, and developability constraints.
    • Served as a technical bridge between computation and experimental teams, translating FEP trends, MD-derived conformational insights, virtual screening, and machine learning results into actionable hypotheses that directly informed synthesis and experimental prioritization.
  • 2021 - 2025

    Frederic, MD, US

    Postdoctoral Fellow | Research Fellow
    National Cancer Institute, National Institute of Health
    • Independently led multiple structure- and mechanism-driven discovery efforts in cancer signaling, driving hypothesis formation, computational strategy, and interpretation across protein–ligand and protein–protein interaction systems.
    • Developed reusable computational pipelines integrating MD-based conformational sampling with free-energy analyses (MM/GBSA, FEP) to enable systematic evaluation across multiple targets and ligand series.
    • Identified cryptic and allosteric binding pockets via MD-driven conformational exploration, informing inhibitor and PROTAC design strategies.
    • Applied AI-based protein structure prediction tools (AlphaFold, RoseTTAFold) to generate working models for proteins and protein–protein complexes in the absence of experimental structures, enabling downstream modeling and interaction analysis.
  • 2017 - 2021

    Akron, OH, US

    Research Assistant
    The University of Akron
    • Built computational chemistry and biology pipelines to model protein–protein, protein–ligand, protein–membrane, and peptide interactions, supporting small-molecule and peptide-based therapeutic design.
    • Applied molecular docking and MD simulations to characterize binding mechanisms and conformational behavior, guiding structure- and sequence-level optimization.
    • Developed ML/AI models to predict sequence/structure–property relationships for peptides, small molecules, and biofunctional materials, working closely with experimental collaborators for validation.

Publications

  • 2025
    mTOR variants activation discovers PI3K-like cryptic pocket, expanding allosteric, mutant-selective inhibitor designs
    American Chemical Society

    Dysregulated mechanistic target of rapamycin (mTOR) signaling is implicated in various human diseases, including cancer and neurological disorders. Here, we investigate the structural dynamics of mTOR variants associated with hyperactivation, revealing a cryptic pocket akin to that in phosphoinositide 3-kinases (PI3Ks). Our findings suggest new avenues for designing allosteric, mutant-selective inhibitors targeting this cryptic site, potentially enhancing therapeutic strategies against mTOR-driven pathologies.

Skills

Programming & Scientific Computing (Master): Python, R, Java, Fortran, HPC environments
Molecular Modeling & Simulation & Cheminformatics (Master): RDKit, OpenMM, NAMD, CHARMM, Schrödinger, AutoDock Vina, PyMOL, GROMACS, AMBER, MOE, Chimera, VMD
Machine Learning & Deep Learning (Master): scikit-learn, TensorFlow, Keras, PyTorch, XGBoost, DeepChem, HuggingFace, AlphaFold, RoseTTAFold, DiffDock, ProteinMPNN, RFdiffusion

Languages

Chinese (Mandarin) : Native speaker
English : Fluent

Interests

Data Science & Artificial Intelligence: Machine Learning, Deep Learning, Natural Language Processing, Computer Vision, Generative Models, Reinforcement Learning, Transfer Learning, Explainable AI
Drug Discovery & Computational Chemistry: Molecular Dynamics Simulation, Molecular Docking, QSAR Modeling, Pharmacophore Modeling, Free Energy Calculations, Cheminformatics, Structure-Based Drug Design, Ligand-Based Drug Design
Drug Design & Structural Biology: Protein Structure Prediction, Protein-Protein Interactions, Protein-Ligand Interactions, Homology Modeling

Certificates

  • Data Scientist - Dataquest
  • Natural Language Processing (NLP) with Attention Models - Coursera
  • Natural Language Processing (NLP) with Probabilistic Models - Coursera
  • Natural Language Processing (NLP) with Sequence Models - Coursera
  • Natural Language Processing (NLP) with Classification and Vector Spaces - Coursera
  • Convolutional Neural Networks (CNN) - Coursera

Projects

  • End-to-End Alchemical Free Energy Perturbation (FEP) Pipeline for Ligand Binding Affinity Prediction
    • Designed and implemented an end-to-end alchemical FEP pipeline using OpenMM, openmmtools, and MBAR, enabling automated prediction of ligand binding affinities in real protein–ligand discovery projects.
    • Built a reproducible workflow covering protein preparation, ligand mapping, alchemical transformations, solvation, equilibration, production MD, and free energy analysis, supporting consistent and auditable computational decision-making.
    • Developed Python utilities and a lightweight dashboard to visualize ΔΔG values, uncertainty estimates, and simulation QC metrics, enabling rapid compound comparison and prioritization across ligand series in real design cycles.
    • Applied the pipeline to real medicinal chemistry use cases, demonstrating its value in guiding structure-based lead optimization and reducing reliance on heuristic scoring functions.
  • Machine Learning–Driven Peptide Design & Experimental Validation
    • Built ML models to identify and design self-assembling peptides with anti-amyloid properties, targeting amyloid-related diseases including Alzheimer’s disease and type 2 diabetes.
    • Represented peptide physicochemical properties using NNAAIndex-based descriptors and performed feature analysis to identify determinants of aggregation behavior.
    • Trained and optimized SVM models (Python, GridSearchCV) to discriminate self-assembling versus non-assembling peptides.
    • Collaborated with experimental teams to validate predictions, resulting in five confirmed peptides with strong anti-amyloid activity, including one patented peptide [Authorized patent (ZL201410100022.5)].
  • Protein Kinase Structural Selectivity Analytics
    • Curated and analyzed 6,700+ protein–ligand complex structures from the PDB to characterize structural determinants of binding site accessibility.
    • Developed structural clustering and network-based analytics to differentiate drug-accessible regions across related protein families.
    • Contributed to development of the KDS (Kinase Drug Selectivity) software platform.

References

  • Professor Ruth Nussinov

    Senior Investigator and Head, Computational Structural Biology Section at Cancer Innovation Laboratory, National Cancer Institute, National Institutes of Health.

  • Professor Jie Zheng

    Regent Distinguished Research Professor, Biomedical Engineering and Chemical Engineering, The University of Texas at San Antonio