Bajad NG, Rayala S, Gutti G, Sharma A, Singh M, Kumar A, Singh SK (2021) Systematic review on role of structure based drug design (SBDD) in the identification of anti-viral leads against SARS-Cov-2. Curr Res Pharmacol Drug Discov 2:100026

Article  PubMed  PubMed Central  Google Scholar 

Jorgensen WL (2004) The many roles of computation in drug discovery. Science 303(5665):1813–1818

Article  CAS  PubMed  Google Scholar 

De Vivo M (2011) Bridging quantum mechanics and structure-based drug design. Front Biosci 16(5):1619–1633

Article  Google Scholar 

Schneider G (2010) Virtual screening: an endless staircase? Nat Rev Drug Discov 9(4):273–276

Article  CAS  PubMed  Google Scholar 

Ain QU, Aleksandrova A, Roessler FD, Ballester PJ (2015) Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening. Wiley Interdiscip Rev Comput Mol Sci 5(6):405–424

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jorgensen WL (2009) Efficient drug lead discovery and optimization. Acc Chem Res 42(6):724–733

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jakhar R, Dangi M, Khichi A, Chhillar AK (2020) Relevance of molecular docking studies in drug designing. Curr Bioinform 15(4):270–278

Article  CAS  Google Scholar 

De Vivo M, Masetti M, Bottegoni G, Cavalli A (2016) Role of molecular dynamics and related methods in drug discovery. J Med Chem 59(9):4035–4061

Article  PubMed  Google Scholar 

Hollingsworth SA, Dror RO (2018) Molecular dynamics simulation for all. Neuron 99(6):1129–1143

Article  CAS  PubMed  PubMed Central  Google Scholar 

Beckstein O, Sansom MS (2006) A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor. Phys Biol 3(2):147

Article  CAS  PubMed  Google Scholar 

Marino KA, Shang Y, Filizola M (2018) Insights into the function of opioid receptors from molecular dynamics simulations of available crystal structures. Br J Pharmacol 175(14):2834–2845

Article  CAS  PubMed  Google Scholar 

Freddolino PL, Arkhipov AS, Larson SB, McPherson A, Schulten K (2006) Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure 14(3):437–449

Article  CAS  PubMed  Google Scholar 

Li J, Flick F, Verheugd P, Carloni P, Lüscher B, Rossetti G (2015) Insight into the mechanism of intramolecular inhibition of the catalytic activity of sirtuin 2 (SIRT2). PLoS One 10(9):e0139095

Article  PubMed  PubMed Central  Google Scholar 

Pantsar T, Rissanen S, Dauch D, Laitinen T, Vattulainen I, Poso A (2018) Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling. PLoS Comput Biol 14(9):e1006458

Article  PubMed  PubMed Central  Google Scholar 

Salo-Ahen OM, Alanko I, Bhadane R, Bonvin AM, Honorato RV, Hossain S, Juffer AH, Kabedev A, Lahtela-Kakkonen M, Larsen AS (2020) Molecular dynamics simulations in drug discovery and pharmaceutical development. Processes 9(1):71

Article  Google Scholar 

Borhani DW, Shaw DE (2012) The future of molecular dynamics simulations in drug discovery. J Comput Aided Mol Des 26:15–26

Article  CAS  PubMed  Google Scholar 

Coop A, MacKerell A (2002) The future of opioid analgesics. Am J Pharm Educ 66(2):153–156

Google Scholar 

Healy JR, Bezawada P, Shim J, Jones JW, Kane MA, MacKerell AD Jr, Coop A, Matsumoto RR (2013) Synthesis, modeling, and pharmacological evaluation of UMB 425, a mixed μ agonist/δ antagonist opioid analgesic with reduced tolerance liabilities. ACS Chem Neurosci 4(9):1256–1266

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shaw DE, Grossman J, Bank JA, Batson B, Butts JA, Chao JC, Deneroff MM, Dror RO, Even A, Fenton CH (2014) Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer. In: SC’14: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. IEEE, New York, pp 41–53

Harvey MJ, De Fabritiis G (2015) AceCloud: molecular dynamics simulations in the cloud. ACS Publications, Washington

Google Scholar 

Kondratyuk N, Nikolskiy V, Pavlov D, Stegailov V (2021) GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP. Int J High Perform Comput Appl 35(4):312–324

Article  Google Scholar 

Turalija M, Petrović M, Kovačić B (2022) Towards general-purpose long-timescale molecular dynamics simulation on exascale supercomputers with data processing units. In: 2022 45th Jubilee International Convention on Information, Communication and Electronic Technology (MIPRO), IEEE, New York, pp 300–306

Harvey MJ, Giupponi G, Fabritiis GD (2009) ACEMD: accelerating biomolecular dynamics in the microsecond time scale. J Chem Theory Comput 5(6):1632–1639

Article  CAS  PubMed  Google Scholar 

Alam S, Varettoa U (2014) GROMACS on Hybrid CPU-GPU and CPU-MIC clusters: preliminary porting experiences, results and next steps

Bergdorf M, Robinson-Mosher A, Guo X, Law KH, Shaw DE (2021) Desmond/GPU performance as of April 2021. DE Shaw Research, Tech. Rep. DESRES/TR–2021-01

Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turoňová B, Zimmerli CE, Buczak K, Schmidt FH, Margiotta E, Mackmull M-T (2022) AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science 376(6598):eabm9506

Article  CAS  PubMed  Google Scholar 

Nawrocki G, Im W, Sugita Y, Feig M (2019) Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending. Proc Natl Acad Sci 116(49):24562–24567

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pezeshkian W, König M, Wassenaar TA, Marrink SJ (2020) Backmapping triangulated surfaces to coarse-grained membrane models. Nat Commun 11(1):2296

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stevens JA, Grünewald F, van Tilburg PM, König M, Gilbert BR, Brier TA, Thornburg ZR, Luthey-Schulten Z, Marrink SJ (2023) Molecular dynamics simulation of an entire cell. Front Chem 11:1106495

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luthey-Schulten Z, Thornburg ZR, Gilbert BR (2022) Integrating cellular and molecular structures and dynamics into whole-cell models. Curr Opin Struct Biol 75:102392

Article  CAS  PubMed  Google Scholar 

Perilla JR, Goh BC, Cassidy CK, Liu B, Bernardi RC, Rudack T, Yu H, Wu Z, Schulten K (2015) Molecular dynamics simulations of large macromolecular complexes. Curr Opin Struct Biol 31:64–74

Article  CAS  PubMed  PubMed Central  Google Scholar 

Skånberg R, Linares M, König C, Norman P, Jönsson D, Hotz I, Ynnerman A (2018) VIA-MD: Visual interactive analysis of molecular dynamics. In: MolVa@ EuroVis, pp 19–27

Magarkar A (2023) MD-Simba. https://github.com/aniketsh/MD-SIMBA-Public (accessed) 2020

Blaschke T, Arús-Pous J, Chen H, Margreitter C, Tyrchan C, Engkvist O, Papadopoulos K, Patronov A (2020) REINVENT 2.0: an AI tool for de novo drug design. J Chem Inf Model 60(12):5918–5922

Article  CAS  PubMed  Google Scholar 

Glaser J, Vermaas JV, Rogers DM, Larkin J, LeGrand S, Boehm S, Baker MB, Scheinberg A, Tillack AF, Thavappiragasam M (2021) High-throughput virtual laboratory for drug discovery using massive datasets. Int J High Perform Comput Appl 35(5):452–468

Article  Google Scholar 

Scientific O (2019) GigaDocking™—structure based virtual screening of over 1 billion molecules webinar

Rogers DM, Agarwal R, Vermaas JV, Smith MD, Rajeshwar RT, Cooper C, Sedova A, Boehm S, Baker M, Glaser J (2023) SARS-CoV2 billion-compound docking. Sci Data 10(1):173

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boby ML, Fearon D, Ferla M, Filep M, Koekemoer L, Robinson MC, Consortium CM, Chodera JD, Lee AA, London N (2023) Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science 382(6671):eabo7201

Article