Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model

Do P-C et al (2020) iBRAB: in silico based-designed broadspectrum fab against H1N1 influenza a virus. PLoS ONE 15:e0239112

Article  CAS  PubMed  PubMed Central  Google Scholar 

Is the world ready to respond to the next influenza pandemic? in Exploring lessons learned from a century of outbreaks: readiness for 2030. (2019) National Academies

Taubenberger JK, Morens DM (1918): The Mother of all pandemics. Emerging Infectious Diseases, 2006. 12(1): p. 8

Stuart-Harris CH, Schild GC (1958) Influenza: the viruses and the disease. Edward Arnold

Cox NJ, Subbarao K (2000) Global epidemiology of influenza: past and Present. Annu Rev Med 51:407–421

Article  CAS  PubMed  Google Scholar 

Jong JCFD et al (1997) A pandermic warning? Nature 389(554):1

Google Scholar 

Lee N et al (2003) A major ourbreak of severe acute raspiratoty syndrome in Hong Kong. N Engl J Med 348(20):9

Article  Google Scholar 

Ali MG et al (2020) Recent advances in therapeutic applications of neutralizing antibodies for virus infections: an overview. Immunol Res 68:325–339

Article  CAS  PubMed  PubMed Central  Google Scholar 

Walker LM, Burton DR (2018) Passive immunotherapy of viral infections: ‘super-antibodies’ enter the fray. Nat Rev Immunol 18:297–308

Article  CAS  PubMed  PubMed Central  Google Scholar 

Regazzi M, Golay J, Molinaro M (2020) Monoclonal antibody monitoring: clinically relevant aspects, a systematic critical review. Ther Drug Monit, 42

Tang Y, Cao Y (2021) Modeling pharmacokinetics and pharmacodynamics of therapeutic antibodies: Progress, challenges, and future directions. Pharmaceutics, 13(3)

Do P-C, Le EH, Le L (2018) Steered molecular dynamics simulation in rational drug design. J Chem Inf Model 58:1473–1482

Article  CAS  PubMed  Google Scholar 

Izrailev S et al (1997) Computational Molecular dynamics: challenges, methods, ideas. Lecture Notes Comput Sci Eng 4:39–65

Article  Google Scholar 

Moldovan L et al (2023) Biomembrane Force Probe (BFP): designs, advancements and recent applications to live-cell mechanobiology. Authorea

Halma MTJ, Tuszynski JA, Wuite GJL (2023) Optical tweezers for drug discovery. Drug Discovery Today 28(1):1–12

Article  Google Scholar 

Kurland NE, Drira Z, Yadavalli VK (2012) Measurement of nanomechanical properties of biomolecules using atomic force microscopy. Micron 43(2–3):116–128

Article  CAS  PubMed  Google Scholar 

Cheong L-Z et al (2019) Lab on a tip: applications of functional atomic force microscopy for the study of electrical properties in biology. Acta Biomater 99:33–52

Article  CAS  PubMed  Google Scholar 

Shao Z et al (1996) Biological atomic force microscopy: what is achieved and what is needed. Adv Phys 45(1):1–86

Article  CAS  Google Scholar 

Pleshakova TO et al (2018) Atomic Force Microscopy for protein detection and their physicoсhemical characterization. Int J Mol Sci 19(4):1142

Article  PubMed  PubMed Central  Google Scholar 

Suna H, Wang J (2013) Novel perspective for protein–drug interaction analysis: atomic force microscope. Analyst 148:454–474

Article  Google Scholar 

Chan R, Chen V (2004) Characterization of protein fouling on membranes: opportunities and challenges. J Membr Sci 242(1–2):169–188

Article  CAS  Google Scholar 

Lu H, Schulten K (1999) Steered molecular dynamics simulations of force-induced protein domain unfolding. Proteins 35:453–463

Article  PubMed  Google Scholar 

Vassiliev S, Zaraiskaya T, Bruce D (2012) Exploring the energetics of water permeation in photosystem II by multiple steered molecular dynamics simulations. Biochim et Biophys Acta (BBA) - Bioenergetics 1817(9):1671–1678

Article  CAS  Google Scholar 

Thapa KB, Katti KS, Katti DR (2020) Compression of Na–montmorillonite swelling clay interlayer is influenced by fluid polarity: a steered molecular dynamics study. Langmuir 36(40):11742–11753

Article  CAS  PubMed  Google Scholar 

Prins JF et al (1999) A virtual environment for steered molecular dynamics. Future Generation Comput Syst 15(4):485–495

Article  Google Scholar 

Thapa KB, Katti KS, Katti DR (2023) Influence of the fluid polarity on shear strength of sodium montmorillonite clay: A steered molecular dynamics study. Comput Geotech, 158

Chandar NB, Lo R, Ganguly B (2014) Quantum chemical and steered molecular dynamics studies for one pot solution to reactivate aged acetylcholinesterase with alkylator oxime. Chemico-Biol Interact 223:58–68

Article  CAS  Google Scholar 

Oliveira GS et al (2019) Immobilization and unbinding investigation of the antigen-antibody complex using theoretical and experimental techniques. J Mol Graph Model 86:219–227

Article  CAS  PubMed  Google Scholar 

Nguyen H et al (2021) Electrostatic interactions explain the higher binding affinity of the CR3022 antibody for SARS-CoV-2 than the 4A8 antibody. B: Biophys Biochem Syst Processes 125(27):7368–7379

CAS  Google Scholar 

Tian F et al (2021) Mutation N501Y in RBD of Spike Protein Strengthens the Interaction between COVID-19 and its Receptor ACE2. eLife

Taka E et al (2021) Critical interactions between the SARS-CoV-2 spike glycoprotein and the human ACE2 receptor. B: Biophys Biochem Syst Processes 125(21):5537–5548

CAS  Google Scholar 

Ngo ST et al (2021) Thermodynamics and kinetics in antibody resistance of the 501Y.V2 SARS-CoV-2 variant. RSC Adv 11:33438–33446

Article  CAS  PubMed  PubMed Central  Google Scholar 

Abidi M, Soheilifard R, Ghasemi RH (2022) Comparison of the unbinding process of RBD-ACE2 complex between SARS-CoV-2 variants (Delta, delta plus, and Lambda): A steered molecular dynamics simulation. Molecular Simulation, 48(18)

Nguyen H et al (2022) Cocktail of REGN antibodies binds more strongly to SARS-CoV-2 than its components, but the Omicron variant reduces its neutralizing ability. B: Biophys Biochem Syst Processes 126(15):2812–2823

CAS  Google Scholar 

Ray D, Quijano RN, Andricioaei I (2022) Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies. Chem Sci 13:7224–7239

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pettersen EF et al (2004) UCSF Chimera—A visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612

Article  CAS  PubMed  Google Scholar 

Vries SJ, Dijk, Bonvin AMJJ (2010) The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 5:883–897

Article  PubMed  Google Scholar 

Zundert GCPv et al (2016) The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J Mol Biol 428(4):720–725

Article  PubMed  Google Scholar 

Honorato RV et al (2021) Structural biology in the clouds: the WeNMR-EOSC ecosystem. Front Mol Biosci, 8

Eswar N et al (2008) Protein structure modeling with MODELLER, in structural proteomics - high-throughput methods. Humana, pp 145–159. B. Kobe, M. Guss, and T. Huber, Editors

Dunbar J et al (2016) SAbPred: a structure-based antibody prediction server. Nucleic Acids Res 44:W474–W478

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pronk S et al (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29:845–854

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lemkul JA, Bevan DR (2010) Assessing the stability of Alzheimer’s amyloid protofibrils using molecular dynamics. J Phys Chem B 114:1652–1660

Article  CAS  PubMed  Google Scholar 

Pham HA, Truong DT, Li MS (2021) Dependence of work on the pulling speed in mechanical ligand unbinding. J Phys Chem B 125:8325–8330

Article  CAS  PubMed  PubMed Central  Google Scholar 

Systèmes DB (2019) Discovery Studio Modeling Environment, Release 2019

Campbell M, Essential R (2019) Packages: Tidyverse. Learn RStudio IDE. A, Berkeley, CA, pp 63–72

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