GROMACS - Molecular dynamics package primarily designed for simulations of proteins, lipids, and nucleic acids.
NAMD - High-performance molecular dynamics program designed for large biomolecular systems.
LAMMPS - Molecular dynamics software for simulating atoms or molecules, with a focus on materials science.
AMBER - Software package for molecular dynamics of biomolecules, commonly used for proteins and nucleic acids.
CHARMM - Chemistry at HARvard Macromolecular Mechanics for molecular dynamics simulations.
Quantum Chemistry and Electronic Structure
Gaussian - Software for computational chemistry and quantum mechanical calculations.
ORCA - Electronic structure package with a focus on ab initio quantum chemistry calculations.
Q-Chem - Comprehensive quantum chemistry package for electronic structure calculations.
GAMESS - General Atomic and Molecular Electronic Structure System for ab initio quantum chemistry.
DNA and RNA Nanotechnology
NUPACK - Suite for nucleic acid sequence design, analysis, and simulation of DNA and RNA structures.
ViennaRNA - RNA secondary structure prediction and comparison tools based on dynamic programming.
Mfold - Software for RNA and DNA secondary structure prediction.
Unafold - Software for nucleic acid folding, hybridization prediction, and melting temperature calculations.
DNA Strand Displacement
Dsd - DNA strand displacement modeling and analysis tool for designing and analyzing DNA strand displacement reactions.
Visual DSD - Microsoft’s visual design tool for DNA strand displacement systems, supporting the design and simulation of DNA-based computational circuits.
Peppercorn - Tool for analyzing DNA strand displacement reactions through thermodynamic analysis and reaction pathways.
Molecular Design and Synthetic Biology
Cello - Genetic circuit design tool that converts high-level logic to DNA sequences.
GENE Designer - Tool for designing synthetic DNA sequences with complex regulatory structures.
Benchling - Cloud-based platform for DNA sequence analysis, CRISPR design, and other molecular biology applications.
Protein Design
Rosetta - Suite for protein structure prediction, design, and protein-ligand docking.
FoldX - Tool for protein design and stability analysis, assessing the impact of mutations on protein structure.
Phenix - Comprehensive software suite for macromolecular structure determination through X-ray crystallography and cryo-EM.
Visualization
PyMOL - Molecular visualization system used for 3D rendering of small molecules and biological macromolecules.
Chimera - Visualization and analysis software for interactive molecular modeling.
VMD (Visual Molecular Dynamics) - Tool for displaying and analyzing molecular dynamics simulations and molecular structures.
DNA/Protein Structure Analysis
BLAST - Basic Local Alignment Search Tool for comparing biological sequences.
Clustal Omega - Tool for multiple sequence alignment of DNA, RNA, or protein sequences.
HMMER - Software for searching sequence databases with protein or nucleotide sequence profiles.
Synthetic Biology and Metabolic Pathway Engineering
COBRA Toolbox - MATLAB-based toolbox for constraint-based analysis of genome-scale models in systems biology.
SynBioCAD - Computer-aided design tool for synthetic biology workflows, including metabolic pathway design.
OptFlux - Software for metabolic engineering simulation and optimization based on stoichiometric models.