Estimation of Ligand Efficacies of Metabotropic Glutamate Receptors from Conformational Forces Obtained from Molecular Dynamics Simulations. - Sirish Kaushik Lakkaraju; Fengtian Xue; Alan I. Faden; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2013)

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach. - E. Prabhu Raman; Wenbo Yu 002; Sirish Kaushik Lakkaraju; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2013)

Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. - Wenbo Yu 002; Sirish Kaushik Lakkaraju; E. Prabhu Raman; Alexander D. MacKerell Jr. (J. Comput. Aided Mol. Des., 2014)

Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors. - Sirish Kaushik Lakkaraju; Wenbo Yu 002; E. Prabhu Raman; Alena V. Hershfeld; Lei Fang; Deepak Deshpande; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2015)

Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules. - Wenbo Yu 002; Sirish Kaushik Lakkaraju; E. Prabhu Raman; Lei Fang; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2015)

DIRECT-ID: An automated method to identify and quantify conformational variations - application to β2-adrenergic GPCR. - Sirish Kaushik Lakkaraju; Justin A. Lemkul; Jing Huang 004; Alexander D. MacKerell Jr. (J. Comput. Chem., 2016)

Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches. - E. Prabhu Raman; Sirish Kaushik Lakkaraju; Rajiah Aldrin Denny; Alexander D. MacKerell Jr. (J. Comput. Chem., 2017)

Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. - Vincent D. Ustach; Sirish Kaushik Lakkaraju; Sunhwan Jo; Wenbo Yu 002; Wenjuan Jiang; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2019)

Insights into Glucose-6-phosphate Allosteric Activation of β-Glucosidase A. - Anderson A. Gomes; Gustavo F. da Silva; Sirish Kaushik Lakkaraju; Beatriz Gomes Guimarães; Alexander D. MacKerell Jr.; Maria de Lourdes B. Magalhães (J. Chem. Inf. Model., 2021)

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. - Lorenzo D'amore; David F. Hahn; David L. Dotson; Joshua T. Horton; Jamshed Anwar; Ian Craig; Thomas Fox; Alberto Gobbi; Sirish Kaushik Lakkaraju; Xavier Lucas; Katharina Meier; David L. Mobley; et al. (J. Chem. Inf. Model., 2022)

MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics. - Alexander C. Brueckner; Benjamin Shields; Palani Kirubakaran; Alexander Suponya; Manoranjan Panda; Shana L. Posy; Stephen R. Johnson; Sirish Kaushik Lakkaraju (J. Comput. Aided Mol. Des., 2024)