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Our high-performance computing system provides advanced calculations of chemical processes in solution, based on molecular solvation theory and first-principles statistical mechanics. At its core, the 3D-RISM engine enables solvation thermodynamics with efficient, parallelized programs for computational chemistry, drug discovery, material science, and electronic structure calculations.

What we offer

SMModeling, Inc. is a Canadian company located in Edmonton, Alberta.

We provide consulting services of our experts to help design multiple viable solutions to problems of interest using our high throughput computational chemistry and biology software packages.

  • High performance computing codes for advanced calculations
  • Versatility in Application
  • 3D-RISM calculation
  • Full Customer Experience Service

Exclusive 3D-RISM Calculation

  • RISM is based on integral equation theory, modeling the distribution functions of solvent molecules to capture a system’s dynamics. Radial distribution functions (RDFs) describe the probability of finding solvent at a specific distance from a reference point, such as solute molecules, revealing the solvation structure around the solute. We offer validated solvent models for various solvents, prebuilt for seamless integration into research projects.
  • Quasidynamics with 3D-RISM-KH Exclusive to our software,  quaasidynamics are not available in contemporary simulation packages with 3D-RISM.

Our Advantage and Strength

(1) Solvent + Co-solvent + Ions + Additives in a simulation setup – easy to emulate a real-life like situation.   Examples of complex environments are Blood-Brain-Barrier permeability, Inhibitor Binding, and Protein-Ligand Binding .

(2) Easy benchmarking protocol available for a large number of solvents for both biochemical and industrial process applications.

(3) Solvation parameters can be exported to use as descriptors in AI/ML applications in permeator design.

(4) Handling of simulation with concentration gradient in multiple solvents (and solutes) mixtures  makes it ideal for biologics design.

(5) Easy porting of 3D-RISM-KH available with AmberTools (and our custom interfacing) to initiate simulation starting from a molecular structure string as input.

Scientific Advisor Dr. Andriy Kovalenko

Contact: akovalenko@smmodeling.com

Find me on LinkedIn

Publications

3D-RISM Theory

  1. Chandler, D.; McCoy, J. D.; Singer, S. J. J. Chem. Phys., 1986, 85, 5971–5976. DOI: 10.1063/1.451510
  2. Kovalenko, A.; Hirata, F. Chem. Phys. Lett., 1998, 290, 237–244. DOI: 10.1016/S0009-2614(98)00471-0
  3. Kovalenko, A.; Hirata, F. J. Chem. Phys., 1999, 110, 10095–10112. DOI: 10.1063/1.478883
  4. Kovalenko A., Hirata F. J. Chem. Phys., 2000, 112, 10391–10402;10403–10417. DOI: 10.1063/1.481676
  5. Kovalenko, A. Three-dimensional RISM theory for molecular liquids and solid-liquid interfaces. In: Molecular Theory of Solvation. Hirata F. (Ed.), Understanding Chemical Reactivity Series. Vol. 24, Kluwer Academic Publishers, Norwell, 2003, Chapter 4, pp. 169–275.
  6. Gusarov, S.; Ziegler, T.; Kovalenko, A. J. Phys. Chem. A, 2006, 110, 6083–6090. DOI: 10.1021/jp054344t
  7. Gusarov, S.; Pujari B. S.; Kovalenko, A. J. Comput. Chem., 2012, 33, 1478–1494. DOI: 10.1002/jcc.22974
  8. Kovalenko, A. Partial Molar Volumes of Proteins in Solution: Prediction by Statistical–Mechanical, 3D–RISM–KB Molecular Theory of Solvation. In: Volume Properties: Liquids, Solutions and Vapours. Wilhelm, E., Letcher T. (Eds.), Royal Society of Chemistry, Cambridge, 2015, Chapter 22, pp. 575–610. DOI: 10.1039/9781782627043-00575
  9. Roy, D.; Kovalenko, A. 3D-RISM-KH Molecular Solvation Theory. In: Multiscale Dynamics Simulations: Nano and Nano-bio Systems in Complex Environments. Salahub, D. R.; Wei, D. (Eds.), RSC Publishing, London, 2021, Chapter 9, pp. 254–286. ISBN: 978-1-83916-178-0
  10. Roy, D.; Kovalenko, A. Solvation Free Energy by 3D-RISM-KH Theory. In: Gibbs Energy and Helmholtz Energy: Liquids, Solutions and Vapours. Wilhelm, E.; Letcher, T. M. (Eds.) RSC Publishing, London, 2022, Chapter 6, pp. 227–237. ISBN: 978-1-83916-201-5.
  11. Roy, D.; Kovalenko, A. Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory.                Int. J. Molec. Sci., 2021, 22, 5061–14. DOI: 10.3390/ijms22105061

Solvation Free Energy and Solvent Maps with the 3D-RISM-KH Theory (including Ligand Mapping, Molecular Docking, and Molecular Partitioning)

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  1. Stumpe, M. C.; Blinov, N.; Wishart, D.; Kovalenko, A.; Pande, V. S. Calculation of Local Water Densities in Biological Systems – A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation. J. Phys. Chem. B, 2011, 115, 319–328 (Journal Cover).
  2. Imai, T.; Miyashita, N.; Sugita, Y.; Kovalenko, A.; Hirata, F.; Kidera, A. Functionality Mapping on Internal Surfaces of Multidrug Transporter AcrB Based on Molecular Theory of Solvation: Implications for Drug Efflux Pathway. J. Phys. Chem. B, 2011, 115, 8288–8295 (Journal Cover).
  3. Nikolic, D.; Blinov, N.; Wishart, D.; Kovalenko, A. 3D-RISM-Dock: A New Fragment-Based Drug Design Protocol. J. Chem. Theory Comput., 2012, 8, 3356–3372.
  4. Nikolić, D.; Moffat, K. A.; Farrugia, V. M.; Kobryn, A. E.; Gusarov, S.; Wosnick, J. H.; Kovalenko, A. Multi-Scale Modeling and Synthesis of Polyester Ionomers. Phys. Chem. Chem. Phys., 2013, 15, 6128–6138.
  5. Kovalenko, A. Multiscale modeling of solvation in chemical and biological nanosystems and in nanoporous materials. Pure Applied Chem., 2013, 85, 159–199 (Invited Paper).
  6. Huang, W.-J.; Blinov, N.; Wishart, D. S.; Kovalenko, A. Role of Water in Ligand Binding to Maltose-Binding Protein: Insight from a New Docking Protocol Based on the 3D-RISM-KH Molecular Theory of Solvation. J. Chem. Inf. Model., 2015, 55, 317–328.
  7. Omelyan, I.; Kovalenko, A. MTS-MD of biomolecules steered with 3D-RISM-KH mean solvation forces accelerated with generalized solvation force extrapolation. J. Chem. Theory Comput., 2015, 11, 1875–1895.
  8. Kovalenko, A.; Gusarov, S. Multiscale methods framework: self-consistent coupling of molecular theory of solvation with quantum chemistry, molecular simulations, and dissipative particle dynamics. Phys. Chem. Chem. Phys., 2018, 20, 2947–2969 (Invited).
  9. Roy, D.; Kovalenko, A. Performance of 3D-RISM-KH in Predicting Hydration Free Energy: Effect of Solute Parameters. J. Phys. Chem. A, 2019, 123, 4087–4093.
  10. Hinge, V. K.; Roy, D.; Kovalenko, A. Predicting skin permeability using the 3D-RISM-KH theory based solvation energy descriptors for a diverse class of compounds. J. Computer-Aided Mol. Des., 2019, 33, 605–611.
  11. Hinge, V. K.; Roy, D.; Kovalenko, A. Prediction of P-glycoprotein inhibitors with machine learning classification models and 3D-RISM-KH theory based solvation energy descriptors. J. Computer-Aided Molec. Des., 2019, 33, 965–971.
  12. Hinge, V. K.; Blinov, N.; Roy, D.; Wishart, D. S.; Kovalenko, A. The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations. J. Computer-Aided Mol. Des., 2019, 33, 913–926.
  13. Roy, D.; Hinge, V. K.; Kovalenko, A. To Pass or Not To Pass: Predicting the Blood−Brain Barrier Permeability with the 3D-RISM-KH Molecular Solvation Theory. ACS Omega, 2019, 4, 16774–16780.
  14. Roy, D.; Hinge, V. K.; Kovalenko, A. Predicting Blood-Brain Partitioning of Small Molecules Using a Novel Minimalistic Descriptor-Based Approach via the 3D-RISM-KH Molecular Solvation Theory. ACS Omega, 2019, 4, 3055–3060.
  15. Roy, D.; Dutta, D.; Wishart, D. S.; Kovalenko, A. Predicting PAMPA permeability using the 3DRISM-KH theory: Are we there yet? J. Computer-Aided Mol. Des., 2021, 35, 261–269.

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