arXiv subjects

Tyler Luchko

Publications and source records attributed to Tyler Luchko.

5 recordsLinked to original sources

arXiv2026

Solv-eze: Automated Placement of Explicit Water Molecules Using 3D-RISM

Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added from a pre-equilibrated solvent box and removed using conservative steric cutoffs, an approach that can eliminate important interfacial waters that are often not recovered during equilibration due to kinetic barriers limiting exchange with bulk solvent. In this work, we present an automated and computationally efficient method for placing water molecules around biomolecular solutes using three-dimensional reference interaction site model (3D-RISM) solvent density distributions. By identifying regions of high solvent probability, the method generates physically meaningful initial hydration structures without requiring extended sampling or specialized techniques such as grand canonical Monte Carlo (MC) or hybrid MC/MD approaches, and will be released as an update to AmberTools 26, enabling seamless integration into standard MD preparation pipelines. We validated the approach on a diverse set of protein-ligand complexes with crystallographically resolved bridging waters, showing that the method reproduced over 80% of experimentally observed bridging waters and 85% of buried waters not accessible to the bulk. Subsequent energy minimization of both crystallographic and predicted waters further improved agreement. Overall, this method enables more accurate and practical initialization of interfacial hydration, improving the reliability of MD simulations with modest computational cost relative to routine system preparation.

physics.chem-ph↗

arXiv2025

Automated Workflow for Absolute Binding Free Energy Calculations with Implicit Solvent and Double Decoupling

Accurate absolute binding free energy (ABFE) calculations can reduce the time and cost of identifying drug candidates from a diverse pool of molecules that may have been overlooked experimentally. These calculations typically employ explicit solvents; however these models can be computationally demanding and challenging to implement due to the difficulties in sampling waters and managing changes in net charge. To address these challenges, we introduce an automated parallel Python workflow that adopts the double decoupling method, incorporating conformational restraints and pairing it with the implicit generalized Born (GB) solvation model. This approach enhances convergence, reduces computational costs and avoids the technical issues associated with explicit solvents. We applied this workflow to a series of 93 host-guest complexes from the TapRoom database. When pooling all systems, the GB(OBC) model correlated well with experiment ($R^2 = 0.86$); however, this global metric obscured much weaker correlations observed within individual hosts ($R^2 = 0.3-0.8$). Systematic errors associated with charged functional groups (notably ammonium and carboxylates) were also evident, resulting in root-mean-squared errors (RMSEs) greater than 6.12 kcal/mol across all models. Although the GB models did not achieve reliable accuracy across all systems, they may be practical when all ligands contain the same functional groups. Furthermore, a linear correction based on these functional groups reduced RMSE values to within 1 kcal/mol of experiment, and our error analysis suggests specific changes for future GB models to improve accuracy. Overall, the Python workflow demonstrates promise for fast, reliable absolute binding free energy calculations by leveraging the sampling efficiency of GB in a fully automated application.

physics.chem-ph↗

arXiv2025

Development of an Optimized Parameter Set for Monovalent Ions in the Reference Interaction Site Model of Solvation

Accurate modeling of aqueous monovalent ions is essential for understanding the function of biomolecules, such as nucleic acid stability and binding of charged drugs to protein targets. The 1D and 3D reference interaction site models (1D- and 3D-RISM) of molecular solvation, as implemented in the AmberTools molecular modeling suite, are well suited for modeling mixtures of ionic species around biomolecules across a wide range of concentrations. However, the available ion model parameters were optimized for molecular dynamics simulations, not for the RISM framework, which includes a closure approximation. To address this, we optimized the Lennard-Jones 12-6 model for monovalent ions for 1D-RISM with the partial series expansion of order 3 closure by fitting to experimental values of ion-oxygen distance (IOD), hydration free energy (HFE), partial molar volume (PMV) and mean activity coefficient. The new parameter set demonstrated significant improvement in HFE, IOD, and mean activity coefficients, whereas no overall change was observed for the PMV. A second optimization step was necessary to account for the cation-anion interactions that affect the mean activity coefficients. The new parameters were validated at finite salt concentrations against experimental data for 16 ion pairs and showed improved accuracy for 14 of them, while the results for CsI and CsF were the second best. 1D-RISM results obtained with the new NaCl parameters were used to calculate the preferential interaction parameter of the ions around the 24L B-DNA using 3D-RISM. The new parameters demonstrated better agreement with experiment at physiological and higher concentrations. At lower concentrations, the results primarily depended on the closure with little effect from the ion parameters. Overall, the ion parameters specifically developed for RISM show improved accuracy at infinite dilution and finite concentrations.

physics.chem-ph↗

arXiv2021

Accelerating the 3D-RISM theory of molecular solvation with treecode summation and cut-offs

The 3D reference interaction site model (3D-RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such as water and co-ions, around solute molecules. However, 3D-RISM solutions can be expensive to calculate, especially for proteins and other large molecules where calculating the potential energy between solute and solvent requires more than half the computation time. To address this problem, we have developed and implemented treecode summation for long-range interactions and analytically corrected cut-offs for short-range interactions to accelerate the potential energy and long-range asymptotics calculations in non-periodic 3D-RISM in the AmberTools molecular modeling suite. For the largest single protein considered in this work, tubulin, the total computation time was reduced by a factor of 4. In addition, parallel calculations with these new methods scale almost linearly and the iterative solver remains the largest impediment to parallel scaling. To demonstrate the utility of our approach for large systems, we used 3D-RISM to calculate the solvation thermodynamics and density distribution of 7-ring microtubule, consisting of 910 tubulin dimers, over 1.2 million atoms.

physics.comp-ph↗

arXiv2021

Integral equation models for solvent in macromolecular crystals

Solvent can occupy up to ~70% of macromolecular crystals and hence having models that predict solvent distributions in periodic systems could improve in the interpretation of crystallographic data. Yet there are few implicit solvent models applicable to periodic solutes while crystallographic structures are commonly solved assuming a flat solvent model. Here we present a newly-developed periodic version of the 3D-RISM integral equation method that is able to solve for efficiently and describe accurately water and ions distributions in periodic systems; the code can compute accurate gradients that can be used in minimizations or molecular dynamics simulations. The new method includes an extension of the OZ equation needed to yield charge neutrality for charged solutes which requires an additional contribution to the excess chemical potential that has not been previously identified; this is an important consideration for nucleic acids or any other charged system where most or all of the counter- and co-ions are part of the "disordered" solvent. We present of several calculations of protein, RNA and small molecule crystals to show that X-ray scattering intensities and solvent structure predicted by the periodic 3D-RISM solvent model are in closer agreement with experiment than are intensities computed using the default flat solvent model in the refmac5 or phenix refinement programs, with the greatest improvement in the 2 to 4 {\AA} range. Prospects for incorporating integral equation models into crystallographic refinement are discussed.

physics.chem-ph↗