Software
Software and computational tools used across Yildirim Lab research.
TAPERSS
TAPERSS (Theoretical Analyses, Prediction, and Evaluation of RNA Structures from Sequence) is a physics-based 3D RNA structure-prediction framework based on fragment assembly and written in C++.
Developed by Ivan Riveros and Ilyas Yildirim, with initial code from Dr. Kye Won Wang used as a guide.
Simulation & Molecular Modeling
Biomolecular simulation and force-field development.
Simulation CHARMMMolecular mechanics and dynamics for biomolecular systems.
Simulation GROMACSHigh-performance molecular dynamics and trajectory analysis.
Simulation NAMDScalable molecular dynamics for large biomolecular systems.
Simulation GROMOSBiomolecular molecular-dynamics simulation package and force-field ecosystem.
Quantum Chemistry
Electronic-structure calculations and molecular properties.
Quantum GAMESSAb initio molecular electronic-structure calculations.
Quantum Q-ChemElectronic-structure modeling and method development.
Quantum Chemistry NWChemOpen-source computational chemistry package with electronic-structure and molecular-dynamics capabilities.
Visualization & Analysis
Interactive molecular visualization and trajectory analysis.
NMR UCSF SparkyNMR assignment and analysis.
Nucleic Acids 3DNAStructural analysis and rebuilding of nucleic acids.
Cheminformatics Open BabelChemical file conversion and molecular-data utilities.
Visualization GRASPMolecular-surface and electrostatic-potential visualization and analysis.
NMR Analysis NMRPipeProcessing, display, and analysis of multidimensional NMR spectra.
Electrostatics DelPhiPoisson–Boltzmann electrostatics calculations for biomolecular systems.
Plotting gnuplotCommand-line scientific plotting and data visualization.
Plotting Grace2D plotting and data-analysis tool for Unix-like systems.
Editor JOETerminal-based text editor used in Unix/Linux workflows.
Programming & High-Performance Computing
Active coding and scripting in the lab uses Linux/Unix, Perl, AWK, Python, C, and C++. High-performance-computing workflows use batch and scheduler environments including PBS, MOAB, SLURM, and Torque.
