AutoDock4

• MORRIS, Garrett M. et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry, v. 30, n. 16, p. 2785-2791, 2009. Disponível em: https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21256. Acesso em: 17 jul. 2025.​​

• COSCONATI, Sandro et al. Virtual screening with AutoDock: theory and practice. Expert opinion on drug discovery, v. 5, n. 6, p. 597-607, 2010. Disponível em: https://www.tandfonline.com/doi/abs/10.1517/17460441.2010.484460. Acesso em: 17 jul. 2025.

• FORLI, Stefano; OLSON, Arthur J. A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking. Journal of medicinal chemistry, v. 55, n. 2, p. 623-638, 2012. Disponível em: https://pubs.acs.org/doi/abs/10.1021/jm2005145. Acesso em: 17 jul. 2025.

Open Babel

• ​O'BOYLE, Noel M. et al. Open Babel: An open chemical toolbox. Journal of cheminformatics, v. 3, n. 1, p. 33, 2011. Disponível em: https://link.springer.com/article/10.1186/1758-2946-3-33. Acesso em: 17 jul. 2025

AutoDock Vina

• EBERHARDT, Jerome et al. AutoDock Vina 1.2. 0: new docking methods, expanded force field, and python bindings. Journal of chemical information and modeling, v. 61, n. 8, p. 3891-3898, 2021. Disponível em: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00203. Acesso em: 17 jul. 2025.​

• TROTT, O.; OLSON, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, v. 31, n. 2, p. 455–461, 2010. DOI: https://doi.org/10.1002/jcc.21334. Disponível em: https://pubmed.ncbi.nlm.nih.gov/19499576/. Acesso em: 17 jul. 2025.

Avogrado

• ​HANWELL, Marcus D. et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of cheminformatics, v. 4, n. 1, p. 17, 2012. Disponível em: https://link.springer.com/article/10.1186/1758-2946-4-17. Acesso em: 23 jul. 2025.

CGenFF

• ​VANOMMESLAEGHE, Kenno et al. CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields. Journal of computational chemistry, v. 31, n. 4, p. 671-690, 2010. Disponível em: scholar.google.com/scholar?hl=pt-BR&as_sdt=0%2C5&q=CHARMM+General+Force+Field+%28CGenFF%29%3A+A+force+field+for+drug-like+molecules+compatible+with+the+CHARMM+all-atom+additive+biological+force+fields&btnG=#d=gs_cit&t=1753582274815&u=%2Fscholar%3Fq%3Dinfo%3Aa7wZVyYj9WgJ%3Ascholar.google.com%2F%26output%3Dcite%26scirp%3D0%26hl%3Dpt-BR. Acesso em: 23 jul. 2025.

GROMACS

• ABRAHAM, Mark James et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, v. 1, p. 19-25, 2015. Disponível em: https://www.sciencedirect.com/science/article/pii/S2352711015000059. Acesso em: 23 jul. 2025.​

• BEKKER, Henk et al. Gromacs-a parallel computer for molecular-dynamics simulations. In: 4th international conference on computational physics (PC 92). World Scientific Publishing, 1993. p. 252-256. Disponível em: https://research.rug.nl/en/publications/gromacs-a-parallel-computer-for-molecular-dynamics-simulations. Acesso em: 23 jul. 2025.

• BERENDSEN, Herman JC; VAN DER SPOEL, David; VAN DRUNEN, Rudi. GROMACS: A message-passing parallel molecular dynamics implementation. Computer physics communications, v. 91, n. 1-3, p. 43-56, 1995. Disponível em: https://www.sciencedirect.com/science/article/abs/pii/001046559500042E. Acesso em: 23 jul. 2025.

• HESS, Berk et al. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of chemical theory and computation, v. 4, n. 3, p. 435-447, 2008. Disponível em: https://pubs.acs.org/doi/abs/10.1021/ct700301q. Acesso em: 23 jul. 2025.

• LINDAHL, Erik; HESS, Berk; VAN DER SPOEL, David. GROMACS 3.0: a package for molecular simulation and trajectory analysis. Molecular modeling annual, v. 7, p. 306-317, 2001. Disponível em: https://link.springer.com/article/10.1007/s008940100045. Acesso em: 23 jul. 2025.

• PÁLL, Szilárd et al. Tackling exascale software challenges in molecular dynamics simulations with GROMACS. In: Solving Software Challenges for Exascale: International Conference on Exascale Applications and Software, EASC 2014, Stockholm, Sweden, April 2-3, 2014, Revised Selected Papers 2. Springer International Publishing, 2015. p. 3-27. Disponível em: https://link.springer.com/chapter/10.1007/978-3-319-15976-8_1. Acesso em: 23 jul. 2025.

• PRONK, Sander et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, v. 29, n. 7, p. 845-854, 2013. Disponível em: https://academic.oup.com/bioinformatics/article/29/7/845/253065?login=false. Acesso em: 23 jul. 2025

• VAN DER SPOEL, David et al. GROMACS: fast, flexible, and free. Journal of computational chemistry, v. 26, n. 16, p. 1701-1718, 2005. Disponível em: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20291. Acesso em: 23 jul. 2025.