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All Publications

  1. Jendrusch, M., Korbel, J. O., & Sadiq, S. K. (2021) bioRxiv. AlphaDesign: A de novo protein design framework based on AlphaFold. https://doi.org/10.1101/2021.10.11.463937

  2. S. Lyonnais*‡, S.K. Sadiq*‡, C. Lorca-Oró, L. Dufau, S. Nieto Marquez, T. Escriba, N. Gabrielli, X. Tan, M. Ouizougun-Oubari, J. Okoronkwo, M. Reboud-Ravaux, J. M. Gatell, R. Marquet, J.-C. Paillart, A. Meyerhans, C. Tisné, R. J. Gorelick and G. Mirambeau*‡ (2021) Viruses. The HIV-1 nucleocapsid regulates its own condensation by phase-separated activity-enhancing sequestration of the viral protease during maturation, 13 (11), 2312.

  3. S.K. Sadiq‡, A. Muñiz Chicharro, P. Friedrich and R. Wade (2021) J Chem Theor Comp. A multiscale approach for computing gated ligand binding from molecular dynamics and Brownian dynamics simulations. 17,12,7912-7929.

  4. Balogh,  T. Gyöngyösi, I. Timári, M. Herczeg, A. Borbás, S. K. Sadiq‡, K. Fehér‡ and K. E. Kövér‡ (2021) J Chem Inf Model, Conformational analysis of heparin-analogue pentasaccharides by nuclear magnetic resonance spectroscopy and molecular dynamics simulations, 61 (6) 2926-2936.

  5. S.K. Sadiq‡ (2020) Catalysts, Fine-tuning of sequence-specificity by near attack conformations in enzyme-catalyzed peptide hydrolysis, 10 (6) 684.

  6. S.K. Sadiq‡, G. Mirambeau and A. Meyerhans. (2018) AIDS Research and Human Retroviruses. Equilibrium model of drug-modulated GagPol-embedded HIV-1 reverse transcriptase dimerization to enhance premature protease activation, 34 (9) 804-807.

  7. R.G. Douglas, P. Nandekar, J.-E. Aktories, H. Kumar, R. Weber, J. M. Sattler, M. Singer, S. Lepper, S.K. Sadiq, R.C. Wade and F. Frischknecht. (2018) PLoS Biology, Inter-subunit interactions drive divergent dynamics in mammalian and Plasmodium actin filaments, 16 (7) e2005345.

  8. N.J. Bruce*, G. K. Ganotra*, D. B. Kokh*, S. K. Sadiq* and R. C. Wade*. (2018), Current Opinion in Structural Biology. New approaches for computing ligand-receptor binding kinetics, 49:1-10. 

  9. D. A. Schuetz, W. E. A. de Witte, Y. Ch. Wong, B. Knasmueller, L. Richter, R. Bosma, D. B. Kokh, S. K. Sadiq, I. Nederpelt, E. Segala, M. Amaral, D. Guo, D. Andres, L. A. Stoddart, S. Hill, R. M. Cooke, R. Leurs, M. Frech, R. C. Wade, E. C. M. de Lange, A. P. IJzerman, A. Müller-Fahrnow, G. F. Ecker, (2017) Drug Discovery Today. Kinetics for Drug Discovery – An industry driven effort to target drug residence time. 22 (6) 896-911.

  10. E Fleta-Soriano, K Smutná, JP Martinez, CL Oró, SK Sadiq, G Mirambeau, C Lopez-Iglesias, M Bosch, A Pol, M Brönstrup, J Diez and A Meyerhans (2017) Antimicrobial Agents and Chemotherapy, The myxobacterial metabolite Soraphen A inhibits HIV-1 by reducing virus production and altering virion composition. AAC-00739.

  11. Sadiq, S.K. ‡ (2016). Phil Trans R Soc A. Reaction-diffusion basis of retroviral infectivity 374:20160148.

  12. Sadiq, S.K. ‡ and Coveney P.V. (2015). J Chem Theor Comput. Computing the role of near attack conformations in an enzyme-catalyzed nucleophilic bimolecular reaction. 11 
(1), pp 316–324

  13. Venken, T., Voet, A., De Maeyer, M., De Fabritiis, G. and Sadiq, S.K. ‡ (2013). J Chem 
Theor Comput. Rapid conformational fluctuations of disordered HIV-1 fusion peptide in 
solution. 9 (7), 2870–2874.

  14. B. Konnyu, S. K. Sadiq, T. Turanyi, R. Hirmondo, B. Muller, J. Konvalinka, P. V. 
Coveney, H.-G. Krausslich, V. Muller. (2013). PLoS Comp Biol. Gag-Pol Processing during HIV-1 Virion Maturation: A Systems Biology Approach. 9(6): e1003103.

  15.   Sadiq, S.K.*, Guixà-González, R.*, Dainese E., Pastor, M., De Fabritiis, G. and Selent, J. (2013). Curr Med Chem. Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs. 20 (1), 22-38.

  16.   Sadiq, S. K.‡, Noé, F. and De Fabritiis, G. (2012). Proc Natl Acad Sci USA. Kinetic characterization of the critical step in HIV-1 protease maturation. 109 (50), 20449-20454.  

  17.   Wright, D.W.*, Sadiq, S.K.*, De Fabritiis, G. and Coveney, P.V. (2012). J Am Chem Soc. Thumbs down for HIV: Domain level rearrangements do occur in the NNRTI 
bound HIV-1 Reverse Transcriptase. 134 (31), 12885–12888.

  18.   Sadiq, S. K. ‡ Konnyu, B., Muller, V. and Coveney, P.V. (2011) J Phys Chem B. Reaction Kinetics of Catalyzed Competitive Heteropolymer Cleavage, 115, 11017– 
11027.

  19.   Buch, I.*, Sadiq, S. K.* and De Fabritiis, G. (2011). J Chem Theor Comput. Optimizing potential of mean force calculations of standard binding free energy, 7, 1765–1772. 

  20.   Sadiq, S. K.‡ and De Fabritiis, G. (2010). Proteins: Struct Funct Bioinf. Explicit solvent dynamics and energetics of HIV-1 protease flap-opening and closing, 78: 2873–2885.

  21.   Sadiq, S. K., Wright, D. W., Kenway, O. A. and Coveney, P. V. (2010). J Chem Inf Model. Accurate ensemble molecular dynamics binding free energy ranking of 
multidrug-resistant HIV-1 proteases, 50(5), 890–905.

  22.   R. S. Saksena, B. Boghosian, L. Fazendeiro, O. A. Kenway, S. Manos, M. D. Mazzeo, S. K. Sadiq, J. L. Suter, D. Wright, and P. V. Coveney, (2009). Phil Trans R Soc A. 367, 1897, 2557-2571.

  23.   Sadiq, S. K., Mazzeo, M. D., Zasada, S. J., Manos, S., Stoica, I., Gale, C. V., Watson, S. 
J., Kellam, P., Brew, S. and Coveney, P. V. (2008). Phil Trans R Soc A. Patient-specific
simulation as a basis for clinical decision making. 366, 3199-3219.

  24.   Sadiq, S. K., Zasada, S. J., Wright, D., Stoica, I., and Coveney, P. V. (2008). J Chem Inf Model. Automated molecular simulation based binding affinity calculator for ligand- bound HIV-1 proteases. 48, 1909-1919.

  25.   Stoica, I., Sadiq, S. K. and Coveney, P. V. (2008). J Am Chem Soc. Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. 130, 2639-2648.

  26.   Stoica, I., Sadiq, S. K., Gale, C. V. and Coveney., P. V. (2008). Future HIV Ther. Virtual physiological human research initiative; the future for rational HIV treatment design? 2(5), 419-425.

  27.   Sadiq, S. K., Wan, S. and Coveney, P. V. (2007). Biochemistry. Insights into a mutation-assisted lateral drug escape mechanism from the HIV-1 protease active site. 46 (51), 14865 -14877.

  28.   Sadiq, S. K., Zasada, S. J. and Coveney, P. V. (2006). Lecture Notes in Computer Science. Grid assisted ensemble molecular dynamics simulations of HIV-1 proteases reveal novel conformations of the inhibitor saquinavir. LNBI 4216, Berthold, M.R., Glen, R. and Fischer I. (eds.) CompLife 2006, Springer-Verlag, pp.150–161.

  29.   S. K. Sadiq, S. Wan, and P. V. Coveney (2006). Antiviral Ther. Ensemble molecular dynamics of HIV-1 protease with the inhibitor saquinavir: Insights into the molecular basis of drug resistance caused by the G48V and L90M mutations. 11:S151.

  30.   P. V. Coveney, S. K. Sadiq, R. S. Saksena, M. Thyveetil, S. J. Zasada, M. McKeown and S. Pickles (2006). Proceedings of the UK e-Science All Hands Meeting. A lightweight application hosting environment for grid computing. pp.217–224.

  31.   P. V. Coveney, S. K. Sadiq, R. S. Saksena, S. J. Zasada (2006). Proceedings of the UK e- Science All Hands Meeting. Constructing chained molecular dynamics simulations of HIV-1 protease using the application hosting environment. pp.428–431.

* equal contribution, ‡corresponding author

- Richard P. Feynman -

“What I cannot create, I do not understand.”

PUBLICATIONS

Selected Publications

Jendrusch, M., Korbel, J. O., & Sadiq, S. K. (2021) bioRxiv. AlphaDesign: A de novo protein design framework based on AlphaFold. https://doi.org/10.1101/2021.10.11.463937

​

S. Lyonnais*‡, S.K. Sadiq*‡, C. Lorca-Oró, L. Dufau, S. Nieto Marquez, T. Escriba, N. Gabrielli, X. Tan, M. Ouizougun-Oubari, J. Okoronkwo, M. Reboud-Ravaux, J. M. Gatell, R. Marquet, J.-C. Paillart, A. Meyerhans, C. Tisné, R. J. Gorelick and G. Mirambeau*‡ (2021) Viruses. The HIV-1 nucleocapsid regulates its own condensation by phase-separated activity-enhancing sequestration of the viral protease during maturation, 13 (11), 2312.

​

S.K. Sadiq‡, A. Muñiz Chicharro, P. Friedrich and R. Wade (2021) J Chem Theor Comp. A multiscale approach for computing gated ligand binding from molecular dynamics and Brownian dynamics simulations. 17,12,7912-7929.

​

S. Lyonnais*‡, S.K. Sadiq*‡ et al. (2019) bioRxiv, The HIV-1 ribonucleoprotein dynamically regulates its condensate behavior and drives acceleration of protease activity through membrane-less granular phase separation, 528638.

​

Sadiq, S.K. ‡ (2016). Phil Trans R Soc A. Reaction-diffusion basis of retroviral infectivity 374:20160148.

​

Sadiq, S.K. ‡ and Coveney P.V. (2015). J Chem Theor Comput. Computing the role of near attack conformations in an enzyme-catalyzed nucleophilic bimolecular reaction. 11 
(1), pp 316–324

 

Sadiq, S. K.‡, Noé, F. and De Fabritiis, G. (2012). Proc Natl Acad Sci USA. Kinetic characterization of the critical step in HIV-1 protease maturation. 109 (50), 20449-20454. 

​

Wright, D.W.*, Sadiq, S.K.*, De Fabritiis, G. and Coveney, P.V. (2012). J Am Chem Soc. Thumbs down for HIV: Domain level rearrangements do occur in the NNRTI 
bound HIV-1 Reverse Transcriptase. 134 (31), 12885–12888.

 

Sadiq, S. K. ‡ Konnyu, B., Muller, V. and Coveney, P.V. (2011) J Phys Chem B. Reaction Kinetics of Catalyzed Competitive Heteropolymer Cleavage, 115, 11017– 
11027.

​

Sadiq, S. K., Wright, D. W., Kenway, O. A. and Coveney, P. V. (2010). J Chem Inf Model. Accurate ensemble molecular dynamics binding free energy ranking of 
multidrug-resistant HIV-1 proteases, 50(5), 890–905.

 

Stoica, I., Sadiq, S. K. and Coveney, P. V. (2008). J Am Chem Soc. Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. 130, 2639-2648.

 

* equal contribution, ‡corresponding author

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