​Publications:

• Jason E. Sanchez, Govinda B. KC, Julian Franco, William J. Allen, Jesus David Garcia, and Suman Sirimulla* BiasNet: A Model to Predict Ligand Bias Toward GPCR Signaling J. Chem. Inf. Model. 2021 Publication Date:August 16, 2021 https://doi.org/10.1021/acs.jcim.1c00317
• KC, G.B., Bocci, G., Verma, S. et al. A machine learning platform to estimate anti-SARS-CoV-2 activities. Nat Mach Intell 3, 527–535 (2021). https://doi.org/10.1038/s42256-021-00335-w
• Avram S, Bologa CG, Holmes J, Bocci G, Wilson TB, Nguyen DT, Curpan R, Halip L, Bora A, Yang JJ, Knockel J, Sirimulla S, Ursu O, Oprea TI. DrugCentral 2021 supports drug discovery and repositioning. Nucleic Acids Res. 2020 Nov 5:gkaa997. doi: 10.1093/nar/gkaa997. 
• L. Hurley, B. S. Kristal, S. Sirimulla, C. Schweikert and D. F. Hsu, "Multi-Layer Combinatorial Fusion Using Cognitive Diversity," in IEEE Access, vol. 9, pp. 3919-3935, 2021, doi: 10.1109/ACCESS.2020.3047057.
  
• Fratev, Filip; Gutierrez, Denisse A.; Aguilera, Renato J.; sirimulla, suman (2020): Discovery of New AKT1 Inhibitors by Combination of In silico Structure Based Virtual Screening Approaches and Biological Evaluations. Journal of Biomolecular, Structure, and Dynamics, 2020, 1-11.
• ​Fratev, Filip; Sirimulla, Suman; An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains. Nature Scientific Reports Nov 2019 Accepted In press
• X. Zhong, L. Hurley, S. Sirimulla, C. Schweikert, and D. F. Hsu, “Combining multiple ranking systems on the generalized permutation rank space,” in 5th IEEE Data Computing and Intelligence Conference , Nov 2019.
• Govinda KC, Md Mahmudulla Hassan, Suman Sirimulla KinasepKipred: A Predictive Model for Estimating Ligand-Kinase Inhibitor Constant (pKi). bioRxiv 798561; Oct 2019 doi: https://doi.org/10.1101/798561
• Chen J, Jiang S, Wang J, Renukuntla J, Sirimulla S, Chen J. A Comprehensive Review of Cytochrome P450 2E1 for Xenobiotic Metabolism. Drug Metabolism Reviews. 2019 June; doi: 10.1080/03602532.2019.1632889.
• Filip Fratev, Manuel Miranda-Arango, Bryan Lopez, Elvia Padilla,  Suman Sirimulla Discovery of GlyT2 Inhibitors using Structure-based Pharmacophore Screening and Selectivity studies by, FEP+ Calculations ACS Med. Chem. Lett. 2019, 10, 6, 904-910    
• Saugat  Adhikari; Saloni  Daftardar; Filip  Fratev; Miguel  Rivera; Suman Sirimulla; Kenneth Alexander; Sai Hanuman Sagar Boddu "Elucidation of the Orientation of Selected Drugs with 2-Hydroxylpropyl-β-Cyclodextrin Using 2D-NMR Spectroscopy and Molecular Modelling", International Journal of Pharmaceutics, 2018   
• Md Mahmudulla Hassan Daniel Castaneda Mogollon Olac Fuentes suman sirimulla; "DLSCORE: A Deep Learning Model for Predicting Protein-Ligand Binding Affinities", ChemRxiv. Preprint. 2018 https://doi.org/10.26434/chemrxiv.6159143.v1      
• Lois Mendez, Gabriela Henriquez, Suman Sirimulla, and Mahesh Narayan "Looking back, Looking Forward at Halogen Bonding in Drug Discovery" Molecules 2017 22 (9) 1397
• Mathew  Koebel, Aaron Cooper, Grant  Schmadeke, Soyoung Jeon, Mahesh Narayan, Suman  Sirimulla “S---O, S---N sulfur bonding interactions in Protein-Ligand Complexes: Empirical Considerations and Scoring Function” Journal of chemical Information and modeling, 2016, 56 (12), pp 2298–2309
• Deeksha Pal, Venkatesh Kolluru, Balaji Chandrasekhar, Suman Suman, Suman Sirimulla, Mary Ann Sanders, Houda Alatassi, Murali K Ankem and Chendil Damodaran "Targeting aberrant expression of Notch-1 in ALDH+ cancer stem cells in breast cancer" Molecular Carcinogenesis. Accepted: 10/12/2016 doi: [10.1002/mc.22579]
• Mathew Koebel, Grant Schmadeke, Richard G. Posner, Suman Sirimulla "AutoDock VinaXB: Implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina." Journal of Cheminformatics  2016 8:27 
• Suman Suman, Trinath P Das, Suman Sirimulla, Houda Alatassi , Murali Ankem, and Chendil Damodaran "Withaferin-A suppress AKT induced tumor growth in colorectal cancer cells " Oncotarget  2016 DOI: 10.18632/oncotarget.7351
• Brandon R Thomas, Lily A Chylek, Joshua Colvin, Suman Sirimulla, Andrew HA Clayton, William S Hlavacek, Richard G Posner "BioNetFit: a fitting tool compatible with BioNetGen, NFsim, and distributed computing environments" Bioinformatics  (2015) doi: 10.1093/bioinformatics/btv655
• Suman Sirimulla, Jake Bailey, Rahulsimhan Vegnesa, Mahesh Narayan, “Halogen interactions in protein-ligand complexes: Implications of halogen bonding in rational drug design.” Journal of Chemical Information and modeling, 2013, 53 (11), pp 2781–2791
• Aswani Dutt Vadlapudi, Ravinder Earla, Ramya Krishna Vadlapatla1, Suman Sirimulla, Jake Brain Bailey, Ashim K. Mitra “Novel Biotinylated Lipid Prodrugs of Acyclovir for the Treatment of Herpetic Keratitis(HK): Transporter Recognition, Tissue Stability and Antiviral Activity” Pharmaceutical Research 05/2013; DOI:10.1007/s11095-013-1059-7
• Suman Sirimulla,  Rituraj Pal, Mrudula Raparla, Jake B. Bailey, Rene Duran,  Alvin M. Altamirano,  William C. Herndon, Mahesh Narayan “Identification of novel nitrosative stress inhibitors by virtual screening and experimental evaluation” Molecular Informatics, 2012, 31: 167–172.
• Jwala Jwala, Sai H.S. Boddu, Sujay Shah, Suman Sirimulla, Dhananjay Pal, and Ashim K. Mitra. “Ocular sustained release nanoparticles containing stereoisomeric dipeptide prodrugs of acyclovir” Journal of Ocular Pharmacology and Therapeutics. 04/2011; 27(2):163-72
• Tanja Pietraβ , Itza Cruz-Campa , Justine Kombarakkaran , Suman Sirimulla , Atta M. Arif , and Juan C. Noveron “Hydrogen Physisorption in Cu(II) metallacycle”, J. Phys. chem. C., 2010, 114 (49), pp 21371-21277. 
• Suman Sirimulla , Maricarmen Lerma and William C. Herndon “Prediction of Partial Molar volumes of amino acids and small peptides: counting atoms versus topological indices”. J. Chem. Inf. Model., 2010, 50 (1), pp 194–204.