Structure of the human marker of self 5-transmembrane receptor CD47 von Fenalti, Gustavo, Villanueva, Nicolas, Griffith, Mark, Pagarigan, Barbra, Lakkaraju, Sirish Kaushik, Huang, Richard Y.-C., Ladygina, Nadia, Sharma, Alok, Mikolon, David, Abbasian, Mahan, Johnson, Jeffrey, Hadjivassiliou, Haralambos, Zhu, Dan, Chamberlain, Philip P., Cho, Ho, Hariharan, Kandasamy

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Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization von Ustach, Vincent D, Lakkaraju, Sirish Kaushik, Jo, Sunhwan, Yu, Wenbo, Jiang, Wenjuan, MacKerell, Alexander D

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Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-H... von MacKerell, Alexander D., Jo, Sunhwan, Lakkaraju, Sirish Kaushik, Lind, Christoffer, Yu, Wenbo

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Exploring protein‐protein interactions using the site‐identification by ligand competitive saturation methodology von Yu, Wenbo, Jo, Sunhwan, Lakkaraju, Sirish Kaushik, Weber, David J., MacKerell, Alexander D.

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Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G‑Protein Coupled Receptors von Lakkaraju, Sirish Kaushik, Yu, Wenbo, Raman, E. Prabhu, Hershfeld, Alena V, Fang, Lei, Deshpande, Deepak A, MacKerell, Alexander D

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Hysteresis-Based Mechanism for the Directed Motility of the Ncd Motor von Lakkaraju, Sirish Kaushik, Hwang, Wonmuk

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Characterization of Mg2+ Distributions around RNA in Solution von Lemkul, Justin A, Lakkaraju, Sirish Kaushik, MacKerell, Alexander D

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Modulation of Elasticity in Functionally Distinct Domains of the Tropomyosin Coiled-Coil von Lakkaraju, Sirish Kaushik, Hwang, Wonmuk

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MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics von Brueckner, Alexander C., Shields, Benjamin, Kirubakaran, Palani, Suponya, Alexander, Panda, Manoranjan, Posy, Shana L., Johnson, Stephen, Lakkaraju, Sirish Kaushik

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Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water von Sun, Delin, Lakkaraju, Sirish Kaushik, Jo, Sunhwan, MacKerell, Alexander D

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Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules von Yu, Wenbo, Lakkaraju, Sirish Kaushik, Raman, E. Prabhu, Fang, Lei, MacKerell, Alexander D

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Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulation... von Lakkaraju, Sirish Kaushik, Raman, E. Prabhu, Yu, Wenbo, MacKerell, Alexander D

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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 sat... von Raman, E. Prabhu, Lakkaraju, Sirish Kaushik, Denny, Rajiah Aldrin, MacKerell, Alexander D.

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Critical buckling length versus persistence length: what governs biofilament conformation? von Lakkaraju, Sirish Kaushik, Hwang, Wonmuk

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Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field von D’Amore, Lorenzo, Hahn, David F., Dotson, David L., Horton, Joshua T., Anwar, Jamshed, Craig, Ian, Fox, Thomas, Gobbi, Alberto, Lakkaraju, Sirish Kaushik, Lucas, Xavier, Meier, Katharina, Mobley, David L., Narayanan, Arjun, Schindler, Christina E. M., Swope, William C., in ’t Veld, Pieter J., Wagner, Jeffrey, Xue, Bai, Tresadern, Gary

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Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling von Yu, Wenbo, Lakkaraju, Sirish Kaushik, Raman, E. Prabhu, MacKerell, Alexander D.

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Conformational Heterogeneity of Intracellular Loop 3 of the μ‑opioid G‑protein Coupled Receptor von Huang, Jing, Lakkaraju, Sirish Kaushik, Coop, Andrew, MacKerell, Alexander D

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DIRECT-ID: An automated method to identify and quantify conformational variations - application to [Beta]^sub 2^-adrenergic GPCR von Lakkaraju, Sirish Kaushik, Lemkul, Justin A, Huang, Jing, MacKerell, Alexander D

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DIRECT‐ID : An automated method to identify and quantify conformational variations—application to β 2 ‐adrenergic GPCR von Lakkaraju, Sirish Kaushik, Lemkul, Justin A., Huang, Jing, MacKerell, Alexander D.

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DIRECT-ID: An automated method to identify and quantify conformational variations-application to β2-adrenergic GPCR von Lakkaraju, Sirish Kaushik, Lemkul, Justin A., Huang, Jing, MacKerell Jr, Alexander D.

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