Sikao Guo, Ph.D.

Computational biophysicist · Research software engineer

Exploring proteins.Building the tools.

I develop computational methods and open-source software to understand how proteins move, interact, and assemble.

Protein modeling · C++ / Python · High-performance computing

Sikao Guo, wearing a blue checked shirt, outdoors — **Sikao Guo, Ph.D.**
Research Engineer · Inria

≈90×Faster parallel simulationNERDSS · 96 CPUs · 20,000-particle benchmark 44,000+Structures benchmarkedioNERDSS structure-to-simulation workflows 9 toolsOne specification. Three interfaces.AutoCLIP · PyMOL, VMD, and the web

Research directions

Questions that drive my work.

Research overview

01Current research

How can we explore beyond one protein structure?

Geometric sampling methods for protein loops, fragments, and disordered regions, coupled to all-atom structural validation.

Protein conformational sampling

02Mechanistic modeling

What makes an assembly grow, stabilize, or remodel?

Mechanistic models linking molecular interactions and spatial organization to clathrin and HIV lattice dynamics.

Biomolecular self-assembly

03Scientific software

How do we make a method useful beyond one study?

Parallel simulation engines, automated model-building workflows, and consistent interfaces that other researchers can use.

Reusable computational methods

Open-source software

Methods you can build on.

All software

Application definition

Validated JSON

PyMOLVMDWeb

One specification to three interfaces · schematic

AutoCLIP

Python · JSON Schema · Web

Generate PyMOL, VMD, and web applications from one reusable specification.

9 structural-biology tools · 3 platforms

Code Docs Case study

Spatial domain decomposition

Communicating simulation domains · schematic

NERDSS-MPI

C++ · MPI · Linux

Scale particle-based reaction-diffusion simulation while checking distributed numerical behavior.

≈90× on 96 CPUs · 20,000-particle benchmark

Code Docs Case study

Structure-to-simulation workflow

PDB / mmCIFStructures

CG modelReactions

NERDSSSimulation

Model construction and simulation · schematic

ioNERDSS

Python · Structural data · PyQt6

Turn PDB/mmCIF structures into coarse-grained models and connect simulation, analysis, and visualization.

44,000+ structures · 3–720-subunit assemblies

Code Docs Case study

Selected publications

From methods to mechanisms.

Papers & preprints

2026

arXivPreprintFirst author

A Unified, Cross-Platform Framework for Automatic GUI and Plugin Generation in Structural Bioinformatics and Beyond

Sikao Guo, Edoardo Sarti, and Frédéric Cazals

Read preprint

2025

Journal of Computational ChemistryJournal articleFirst author

Parallelization of Particle-Based Reaction–Diffusion Simulations Using MPI

Sikao Guo, Nenad Korolija, Kent Milfeld, Adip Jhaveri, Mankun Sang, Yue Moon Ying, and Margaret E. Johnson

Read paper

2023

eLifeJournal articleFirst author

Structure of the HIV Immature Lattice Allows for Essential Lattice Remodeling within Budded Virions

Sikao Guo, Ipsita Saha, Saveez Saffarian, and Margaret E. Johnson

Read paper

About me

Physics, biological questions, and the software in between.

My work has grown from mechanochemical models of molecular motors to biomolecular self-assembly, parallel simulation, and protein conformational sampling. Across these problems, I connect method development with numerical validation and reusable software.

More about my background

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