Sikao Guo
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Research portfolio

Methods, mechanisms, and reusable tools.

Selected projects in protein conformational sampling, biomolecular self-assembly, and scientific software.

Protein backbone sampling: backbone selection, SE(3) exploration, inverse-kinematics loop closure, and all-atom validation.
Conceptual schematic

Molecular modeling · Ongoing research

Protein conformational sampling

A modular C++/Python sampler for protein loops, fragments, and intrinsically disordered regions, paired with explicit all-atom validation.

  • C++
  • Python
  • Protein sampling
  • OpenMM
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NERDSS and ioNERDSS workflow from PDB/mmCIF structures through coarse-grained models and reaction rules to parallel simulation.
Conceptual schematic

Scientific computing · Open source

NERDSS + ioNERDSS

Automated structure-to-simulation workflows and a parallel particle-based reaction-diffusion engine, with numerical validation built in.

  • C++
  • Python
  • MPI
  • HPC
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AutoCLIP workflow from CLI metadata and interface design to a validated JSON specification and VMD, PyMOL, and web applications.
Conceptual schematic

Research software · Open source

AutoCLIP

A Python framework that generates PyMOL, VMD, and web applications from a reusable application specification.

  • Python
  • JSON Schema
  • PyMOL
  • VMD
  • Web
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Biomolecular assembly models of clathrin, HIV-1, and dynamin, linking structural constraints to mechanistic models and system-level predictions.
Conceptual schematic

Computational biophysics · Published research

Biomolecular assembly models

Mechanistic models of clathrin and HIV lattices that connect molecular interactions to experimentally observed assembly behavior.

  • Stochastic simulation
  • Self-assembly
  • Membranes
  • Kinetics
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Research & collaboration

Let’s talk about the next question.

I’m interested in molecular-modeling methods, biomolecular simulation, and reusable scientific software.

sikaoguo@gmail.com