Publications


  • Sirish Kaushik Lakkaraju, Justin Lemkul, Alexander D MacKerell,"DIRECT‐ID: An automated method to identify and quantify conformational variations—application to β2‐adrenergic GPCR" J Comput. Chem.2016 37(4):416 [JCC]

  • Sirish Kaushik Lakkaraju, Hannah Mbatia, Marie Hanscom, Zaorui Zhao, Junfang Wu, Bogdan Stoica, Alexander D MacKerell, Alan I Faden, Fengtian Xue,"Cyclopropyl-containing positive allosteric modulators of metabotropic glutamate receptor subtype 5" Bioorgan. Med. Chem. Lett. 2015 25(11):2275 [BMC]

  • Xinhua He, Sirish Kaushik Lakkaraju, Marie Hanscom, Zaorui Zhao, Junfang Wu, Bogdan Stoica, Alexander D MacKerell, Alan I Faden, Fengtian Xue,"Acyl-2-aminobenzimidazoles: A novel class of neuroprotective agents targeting mGluR5" Bioorgan. Med. Chem.2015 23(9):2211[BMC]

  • Sirish Kaushik Lakkaraju, Wenbo Yu, E Prabhu Raman, Alena V Hersfeld, Lei Fang, Deepak A Deshpande, Alexander D MacKerell,"Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors" J. Chem. Info. Model.2015 55(3):700[JCIM]

  • Wenbo Yu, Sirish Kaushik Lakkaraju, E Prabhu Raman, Lei Fang, Alexander D MacKerell, "Pharmacophore modeling using Site-Identification by Ligand COmpetitive Saturation (SILCS) with multiple probe molecules" J. Chem. Info. Model. 2015 55(2):407[JCIM]

  • Sirish Kaushik Lakkaraju, E Prabhu Raman, Wenbo Yu, Alexander D MacKerell, "Sampling of organic solutes in Aqueous and Heterogeneous environments using oscillating chemical potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations" J. Chem. Theory Comput. 2014 10(6):2281[JCTC]

  • Wenbo Yu, Sirish Kaushik Lakkaraju, E Prabhu Raman, Alexander D MacKerell, "Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling" J. Comp. Aided Mol. Des. 2014 28(5):491[JCAMD]

  • E Prabhu Raman, Wenbo Yu, Sirish Kaushik Lakkaraju, Alexander D MacKerell, "Inclusion of multiple fragment types in Site Identification by Ligand Competitive Saturation (SILCS) approach" J. Chem. Inf. Model. 2013 53(12):3384 [JCIM]

  • Sirish Kaushik Lakkaraju, Fengtian Xue, Alan Faden, Alexander D MacKerell, "Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations" J. Chem. Inf. Model. 2013 53(6):1337 [JCIM]

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Hysteresis-based mechanism for the directed motility of the Ncd motor"Biophys. J. 2011 101:1105 [Biophys. J.]

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Critical buckling length versus persistence length: What governs a biofilament conformation?" Phys. Rev. Lett. 2009 102:118102 [PRL] (Selected for the Virtual Journal of Biological Physics Research)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Modulation of elasticity in functionally distinct domains of the tropomyosin coiled-coil" Cel. Mol. BioEng. 2009 2:57 [CMBE] (Invited Contribution)


Conference Proceedings


  • Sirish Kaushik Lakkaraju, Wenbo Yu, E Prabhu Raman, Alexander D MacKerell, "Mapping Functional Group Requirements of Ligands at the Occluded Binding pocket of Beta2-Adrenergic G-Protein Coupled Receptor using Site-Identificaiton by Ligand Competitive Saturation Simulations", Biophysical Society, 2015. (poster)

  • Wenbo Yu, E Prabhu Raman, Sirish Kaushik Lakkaraju, Lei Fang, Alexander D MacKerell, "Pharmacophore modeling using Site-Identification by Ligand Competitive Saturation with multiple probe molecules", Biophysical Society, 2015. (platform)

  • Meagan C Small, Sirish Kaushik Lakkaraju, E Prabhu Raman, Rodrigo B Andrade, Alexander D MacKerell, "Molecular understanding of the binding of macrolide antibiotics to the Ribosome using Site-Identification by Ligand Competitive Saturation", Biophysical Society, 2015. (poster)

  • Rachita Rai, Fengtian Xue, Alexander D MacKerell, Sirish Kaushik Lakkaraju, "Synthesis and Evaluation of Protein Tyrosine Phosphatase inhibitors by targeting a novel allosteric site", American Chemical Society Fall National Meeting, 2014. (poster)

  • Alexander D MacKerell, E Prabhu Raman, Wenbo Yu, Sirish Kaushik Lakkaraju, Olgun Guvench, " Site Identification by Ligand Competitive Saturation (SILCS): Mapping fragment binding sites including consideration of protein flexibility and fragment desolvation using explicit solvent representation", American Chemical Society Spring National Meeting, 2013. (platform)

  • Sirish Kaushik Lakkaraju, Ashley R McDonald, Alexander D MacKerell, "Quantum Mechanical/Molecular Mechanical simulations: An efficient strategy to calculate vibrational stark shift", American Chemical Society Fall National Meeting, 2012. (poster)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Mechanical coupling of the motor protein Ncd in the microtubule minus-end directed motion", Biomedical Engineering Society National Meeting, 2011. (platform)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Atomistic basis for the directionality and cooperativity of the Ncd motor", The 1st KIAS Conference on Subcellular Dynamics: Emergent behaviors of the mechanical elements in the cell, 2011. (platform)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Role of non-specific attractions in conformational behavior of biofilaments: A case study of α--helices and coiled-coils", Sixth World Congress on Biomechanics, 2010. (platform)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Possible intermediate states in the microtubule minus-end directed movement of the Ncd stalk", Biophysical Society, 2010. (platform)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Transition Pathway of the minus end directed movement of Kinesin-14 Ncd", ASME First Congress of Nanotechnology in Medicine and Biology, 2010. (platform)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Length and sequence dependence of elasticity of α-helices and coiled-coils", ASME Summer Bioconference, 2009. (poster)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Regional variations in flexibilities limit continuum rod description of long coiled-coils" Biophysical Society, 2009. (poster)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Limits in application of linear elasticity theory in characterization of α-helices and filamentous proteins", Biophysical Society, 2008. (poster)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Breakdown of linear elasticity in α-helices", Society of Engineering Science, 2007. (platform)

  • Sirish Kaushik Lakkaraju, Wonmuk Hwang, "Molecular mechanics of α-helices", Cardiovascular Research Institute, 2006. (poster, 3rd prize)

  • Sirish Kaushik Lakkaraju, Anant Joshi, "Supporting mobility using CAMEL-Location Based Services, a case study", Avionics and Communication Engineering, 2004. (platform)