Projects on Nacef Guessaymi

Mon, 01 Jan 0001 00:00:00 +0000

Molecular Dynamics

Simulating protein dynamics.

PythonBashSLURMHPCGitpixiconda-forgeSciPyUMAPHDBSCANMDAnalysispytrajOpenMMOpenFF ToolkitOpenFF InterchangeopenmmforcefieldsAMBERRDKitPDBFixerAmberToolsNumPyMatplotliblogurupytestRuffbasedpyrightMkDocsmkdocstringsGitHub Actionsrattler-buildsetuptools-scm

I run molecular dynamics simulations on protein systems, with a focus on amyloid aggregation, and build the tooling that supports that work. Each simulation generates a long trajectory of every atom’s motion, which means a lot of the work is in the analysis — extracting the few measurements that actually mean something from a very large amount of data.

Code → Preprint →

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Mon, 01 Jan 0001 00:00:00 +0000

Computer-Aided Drug Design

Designing small molecules that target systems.

PythonBashSLURMHPCCLI developmentRDKitNumPypandasPolarsZarrmatplotlibscikit-learnumap-learnBitBirchloguruPyYAMLargparsepytestJupyterMkDocsmkdocs-materialmkdocstringsmkdocs-gen-filesmkdocs-jupyterGNINAGypsum-DLReduceFTMapPyMOLChimeraXMol*pixiGitRuffbasedpyrightMolPortUniProt

Antibiotic resistance is outpacing the development of new drugs, and many of the most promising bacterial targets have only recently become structurally tractable. My work builds automated virtual screening pipelines that take a protein structure and a large compound library and return a testable shortlist: docking at scale on HPC clusters, then triage by predicted affinity, chemical diversity, and commercial availability. Each pipeline is released as a documented, reproducible Python package so that screens can be audited, rerun, and redirected at new targets as structures become available.

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Mon, 01 Jan 0001 00:00:00 +0000

Protein Stuctrural Predictions

Predicting protein structures.

PythonBashSLURMHPCBoltz-2Chai-1ColabFold MMseqs2UniProtargparselogururequestsJinja2RDKitPyYAMLSingularityCUDApixi

Many of the proteins worth targeting with new drugs have never had their structures solved experimentally, and without a structure there is little to design against.

I build workflows that predict a protein’s 3D structure directly from its sequence, both on its own and bound to the molecules it naturally interacts with. Each prediction comes with confidence estimates and predicted binding strengths, so much of the work is deciding which models are reliable enough to build on.