Adam Murray - Research
ORCID

Curriculum Vitae

Academic and professional background in computational biology, drug design, and neuroscience.

Education

  • University of California, Santa Cruz January 2024 – June 2026

    Bachelor of Science, Biomolecular Engineering Major / Statistics Minor

    GPA: 3.09

  • Monterey Peninsula College August 2019 – December 2023

    Associate degrees in Chemistry, Mathematics, and Psychology

    GPA: 3.707

  • San Joaquin Valley College April 2012 – June 2013

    Associate of Science, Pharmacy Technology

Research Experience

  • Kim Lab — UC Santa Cruz November 2024 – Present

    Undergraduate Researcher

    Building a from-scratch intrinsic signal imaging macroscope system including optics setup, custom compute workstation, and full stack software development. Quantification and statistical analysis of viral axon tracing, automated cell counting, and Allen Brain Atlas data. Clustering and information-theoretic analysis of datasets.

  • RosettaCommons — UC Davis / Johns Hopkins University September 2023 – Present

    Undergraduate Researcher

    Co-authored computational protein design research with David Baker, 2024 Nobel Prize laureate in Chemistry, focusing on NaV1.7 sodium channel binders. Authored most-read paper in Channels journal for 2024 on ion channel structural modeling using AlphaFold2, RoseTTAFold2, and ESMFold. Engineered novel protein binders for ion channels using state-of-the-art ML techniques including ProteinMPNN and RFDiffusion. Built comprehensive workflows from target input to optimized, validated protein designs.

  • Lokey Lab — UC Santa Cruz September 2022 – Present

    Undergraduate Researcher

    Developed transformer models for molecular property prediction and cheminformatics applications. Created optimization pipelines for peptide library design and combinatorial chemistry. Built analysis pipelines for high-throughput, single-molecule fidelity DEL library assessment. Designed innovative tools for analyzing massive combinatorial library datasets.

  • ACCESS Summer REU — Lokey Lab, UC Santa Cruz June 2022 – August 2022

    Research Intern

    Developed peptide library generation and chemoinformatic analysis utilities as well as a deep learning model for predicting cell membrane permeability of cyclic peptides.

Professional Experience

  • NIH-MARC Program — Santa Cruz, CA August 2025 – Present

    MARC Scholar

  • Unnatural Products — Santa Cruz, CA July 2025 – Present

    Software Consultant

    Profiled internal software and provided comprehensive reports and optimization recommendations.

  • Freelance Consultant/Developer 2019 – Present

    Programming and data analysis consultant for start-ups. Develop pipelines for data analysis, machine learning models, and website designs.

  • Monterey Bay Neurofeedback Center — Carmel, CA November 2018 – May 2023

    Technical Director

    Managed and trained technicians, analyzed EEG time series data using traditional and machine learning based methods, collaborated with doctors to develop treatment plans, maintained hardware, and oversaw buying and implementation of new hardware and software.

Conference Presentations

  • SACNAS NDiSTEM Conference 2023 — Portland, OR October 2023

    "De novo design of peptides targeting the pore domain of Kv1.3 potassium channel."

    Poster Presentation Award Winner

  • RosettaCon 2023 — Leavenworth, WA August 2023

    "De novo design of peptides targeting the pore domain of Kv1.3 potassium channel."

    Poster Presentation Award Winner

  • ACCESS Symposium 2022 — Santa Cruz, CA August 2022

    "Digging Deeper Into Cyclic Peptides: Predicting Permeability of Enumerated Cyclic Peptide Libraries Using Deep Learning."

Teaching & Mentoring

  • Research Peer Mentor — UC Santa Cruz September 2024 – Present

    Working with other undergraduate students, teaching them coding skills, tools, frameworks, methods, theory, and applications in drug design, data analysis, and neuroscience.

  • TRIO Tutor — Monterey Peninsula College February 2023 – September 2023

    Tutored biology, chemistry, computer science, and math during the school semester at the high school level.

  • STEMCEL Tutor — Monterey Peninsula College February 2022 – May 2023

    Tutored biology, chemistry, computer science, and math during the school semester at the collegiate level.

Leadership

  • SACNAS Club Founder — Monterey Peninsula College Fall 2022 – Fall 2023

    Founded club, spearheaded initial paperwork, coordinated acquisition of officers, organized undergraduate research panels, coordinated booths at Family STEM Day, spoke at events to promote the club and SACNAS, and built connections between students and researchers.

  • Engineering and Computer Science Club Co-founder — Monterey Peninsula College Fall 2023

    Co-founded club, worked as lead programmer for MPC STEAM content project, and mentored members in programming, circuit design, and engineering principles.

Technical Skills

Computational Methods

  • Protein/Peptide Design: RoseTTAFold2, AlphaFold2, ESMFold, ProteinMPNN, RFDiffusion, Rosetta Suite
  • Machine Learning: PyTorch, TensorFlow/Keras, Torch Geometric, Scikit-learn, transformers, CNNs, GNNs
  • Molecular Modeling: MOE, ChimeraX, molecular docking, MD simulation, QSAR modeling
  • Mathematical Methods: Statistics, graph theory, signal processing, PCA, wavelet transforms

Programming Languages

  • Expert: Python, C#
  • Proficient: MATLAB, Java, JavaScript, TypeScript, Bash, SQL, R, C++
  • Web Development: React, Node.js, Tailwind, Flask, Three.js
  • GPU Programming: CUDA, OpenCL, WebGL, MPS

Laboratory & Instrumentation

  • Chemistry: Mass spectrometry, HPLC, NMR, organic synthesis, split pool peptide library synthesis
  • Molecular Biology: HMW DNA extraction, sequencing, nanopore sequencing, PCR
  • Imaging: Intrinsic signal imaging, macroscope design, fluorescence microscopy
  • Neuroscience: EEG/ERP analysis, viral tracing quantification, automated cell counting

Specialized Software

  • Bioinformatics: BLAST, UCSC Genome Browser, IGV, JalView, Reactome
  • Cheminformatics: RDKIT, OpenBabel, MDAnalysis, Gromacs, OpenMM
  • Documentation: LaTeX, Markdown, Mermaid
  • Graphics/Game Dev: Godot, Unity, p5.js, Processing