Recent Publications
Reviews and Book Chapters indicated by *
Patents and Patent Applications indicated by **

A Toxoplasma gondii O-glycosyltransferase that Modulates Bradyzoite Cyst Wall Rigidity is Structurally and Functionally Distinct from its Host Homologues
P. Kumar, T. Tomita, T. Gerken, Y. S. Lee, L. Weiss, and N. L. Samara (2023, submitted)

Hemoglobin Variants Increase NOS-dependent Vasodilation of Human Resistance Arteries
S. D. Brooks, A. P. Ruhl, X. Zeng, P. Cruz, S. A. Hassan, O. Kamenyeva, A. Hakim, et al. (2023, submitted)

An Unusual Dual Sugar-binding Lectin Domain Controls Substrate Specificity of a Mucin-type O-Glycosyltransferase
A. M. Collette, S. A. Hassan, S. I. Schmidt, A. J. Lara, W. Yang, N. L. Samara; Science Adv. 10, eadj8829 (2023)

Cannabinoformins: Designing Biguanide-Embedded, Orally Available, Peripherally Selective Cannabinoid-1 Receptor Antagonists for Metabolic Syndrome Disorders
S. Dvoracsko, A. Herrerias, A. Oliverio, P. Bhattacharjee, L. Pommerolle, Z. Liu, D. Feng, Y. S. Lee, S. A. Hassan, G. Godlewski, R. Cinar, and M. R. Iyer; J. Med. Chem. 66, 11985 (2023)

Investigation of Two Zr-p-NO2Bn-DOTA Isomers via NMR and Quantum Chemical Studies
Y. S. Lee, R. D. O’Connor, and O. Vasalatiy; Eur. J. Inorg. Chem. 26, e202300439 (2023)

A Conserved Oligomerization Domain in the Disordered Linker of Coronavirus Nucleocapsid Proteins
H. Zhao, D. Wu, S. A. Hassan, A. Nguyen, J. Chen, G. Piszczek, and P. Schuck; Science Adv. 9, eadg6473 (2023)

Bi-Allelic SNAPC4 Variants Dysregulate Global Alternative Splicing and Lead to Neuroregression and Progressive Spastic Paraparesis
F. G. Frost, M. Morimoto, P. Sharma, L. Ruaud, N. Belnap, D. G. Calame, Y. Uchiyama, N. Matsumoto, M. M. Oud, E. A. Ferreira, V. Narayanan, S. Rangasamy, M. Huentelman, L. T. Emrick, I. Sato-Shirai, S. Kumada, N. I. Wolf, P. J. Steinbach, Y. Huang, Undiagnosed Diseases Network, B. N. Pusey, S. Passemard, J. Levy, S. Drunat, M. Vincent, A. Guet, E. Agolini, A. Novelli, M. C. Digilio, J. A. Rosenfeld, J. L. Murphy, J. R. Lupski, G. Vezina, E. F. Macnamara, D. R. Adams, M. T. Acosta, C. J. Tifft, W. A. Gahl, and M. C. V. Malicdan; Am. J. Hum. Genet. 110, 663 (2023)

A Parasite-encoded Human IL-10 Receptor Antagonist Reveals a Novel Strategy Used to Modulate the Host Response in Filarial Infections
A. Ricciardi, S. A. Hassan, O. Kamenyeva, S. Bennuru, J. Andersen, and T. B. Nutman; Proc. Natl. Acad. Sci. (USA) Nexus 4, 1 (2022)

Newly Identified Disorder of Copper Metabolism Caused by Variants in CTR1, a High-Affinity Copper Transporter
S. Batzios, G. Tal, A.T. DiStasio, Y. Peng, C. Charalambous, P. Nicolaides, E.-J. Kamsteeg, S.H. Korman, H. Mandel, P.J. Steinbach, L. Yi, S.R. Fair, M.E. Hester, A. Drousiotou, and S.G. Kaler; Hum. Mol. Genet. 31, 4121 (2022)

Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets
V. Vishwesh, T. H. Colligan, G. T. Lesica, D. R. Olson, J. Gaiser, C. J. Copeland, T. J. Wheeler, and A. Roy; Front. Pharmacol. 13, 1 (2022)

Plasticity in Structure and Assembly of SARS-CoV-2 Nucleocapsid Protein
H. Zhao, A. Nguyen, D. Wu, Y. Li, S. A. Hassan, J. Chen, H. Shroff, G. Piszczek, and P. Schuck; Proc. Natl. Acad. Sci. (USA) Nexus 1, 1 (2022)

Modulation of Free Energy Landscapes as a Strategy for the Design of Antimicrobial Peptides
S. A. Hassan and P. J. Steinbach; J. Biol. Phys. 48, 151 (2022)

Synthesis, Biological Evaluation, and Molecular Modeling Studies of 3,4-Diarylpyrazoline series of Compounds as Potent, Non-Brain Penetrant Antagonists of Cannabinoid-1 Receptor with Reduced Lipophilicity
M. R. Iyer, R. Cinar, C. Wood, C. N. Zawatsky, N. J. Coffey, K. A. Kim, Z. Liu, A. Katz, S. A. Hassan, and Y. S. Lee; J. Med. Chem. 65, 2374 (2022)

** Cyclic Peptides as Non-Hormonal Contraceptive Agents and Methods of Use Thereof
M. L. Dufau, M. K. Raju, R. Kavarthapu, R. Anbazhagan, and S. A. Hassan; U.S. Patent Application No. 63/250,665 (Sept. 2021); PCT application (Sept. 2022)

Reversion Mutations in Phosphoprotein P of a Codon-pair-deoptimized Human Respiratory Syncytial Virus Confer Increased Transcription, Immunogenicity, and Genetic Stability Without Loss of Attenuation
J. W. Chen, L. Yang, C. Santos, S. A. Hassan, P. L. Collins, U. J. Buchholz, and C. Le Nouen; PLoS Pathog. 17, e1010191 (2021)

Blockade of GRTH/DDX25 Phosphorylation by Cyclic Peptides Provides an Avenue for Developing a Non-Hormonal Male Contraceptive
M. Raju, R. Kavarthapu, R. Anbazhagan, S. A. Hassan, and M. L. Dufau; J. Med. Chem. 64, 14715 (2021)
(supplemental cover)

* Biomolecular Interactions of Ultrasmall Metallic Nanoparticles and Nanoclusters
A. A. Sousa, P. Schuck, and S. A. Hassan; Nanoscale Adv. 3, 2995 (2021)

The Structures of Two Salivary Proteins from the West Nile Vector Culex Quinquefasciatus Reveal a Beta-Trefoil Fold with Putative Sugar Binding Properties
O. Kern, P. C. V. Leon, A. Gittis, B. Bonilla, P. Cruz, A. C. Chagas, S. Ganesan, D. Ribeiro, I. Martin-Martin, and E. Calvo; Curr. Res. Struct. Biol. 3, 95 (2021)

Functional Selectivity of a Biased Cannabinoid-1 Receptor Antagonist
Z. Liu, M. Iyer, G. Godlewski, T. Jourdan, J. Liu, N. Coffey, C. Zawatsky, H. Puhl, J. Wess, J. Meister, J. Liow, R. Innis, S. A. Hassan, Y. S. Lee, G. Kunos, and R. Cinar; ACS Pharmacol. Transl. Sci. 4, 1175 (2021)
(supplemental cover)

Origin of the Stability of Polymethylated DOTA Chelates Complexed with Ln3+ Ions
Y. S. Lee, Z. Mou, A. C. L. Opina, and O. Vasalatiy; Eur. J. Inorg. Chem. 15, 1428 (2021)
(cover illustration)

Functional Anatomy of the Trimer Apex Reveals Key Hydrophobic Constraints That Maintain the HIV-1 Envelope Spike in a Closed State
P. Zhang, A. L. Kwon, C. Guzzo, Q. Liu, H. Schmeisser, H. Miao, Y. Lin, R. Cimbro, J. Huang, M. Connors, S. D. Schmidt, M. A. Dolan, A. A. Armstrong, and P. Lusso; mBio 12, e00090-21 (2021)

DBAASP v3: Database of Antimicrobial/Cytotoxic Activity and Structure of Peptides as a Resource for Development of New Therapeutics
M. Pirtskhalava, A. A. Armstrong, M. Grigolava, M. Chubinidze, E. Alimbarashvili, B. Vishnepolsky, A. Gabrielian, A. Rosenthal, D. E. Hurt, M. Tartakovsky; Nucleic Acids Res. 49, D288 (2021)

** Method for Synthesizing Iodo- or Astatoarenes using Diaryliodonium Salts
F. Guerard, J. F. Gestin, M. W. Brechbiel, and Y. S. Lee; U.S. Patent No. 10858306 for product (granted on December 2020)

** Method for Synthesizing Iodo- or Astatoarenes using Diaryliodonium Salts
F. Guerard, J. F. Gestin, M. W. Brechbiel, and Y. S. Lee; U.S. Patent No. 10703708 for method (granted on July 2020)

Isomerization of Antimalarial Drug WR99210 Explains its Inactivity in a Commercial Stock
T. Remcho, S. Guggilapu, P. Cruz, G. Nardone, G. Heffernan, R. O'Connor, C. Bewley, T. Wellems, and K. Lan; Antimicrob. Agents Chemother. 65, e01385 (2020)

Reply to Comment on "Investigation of Zr(IV) and 89Zr(IV) complexation with hydroxamates: progress towards designing a better chelator than desferrioxamine B immuno-PET imaging"
by A. Bianchi and M. Savastano; Chem. Commun. 56, D0CC01189D (2020)
F. Guerard, Y. S. Lee, R. Tripier, L. P. Szajek, J. R. Deschamps, and M. W. Brechbiel; Chem. Commun. 56, 12667 (2020)

G-Protein Biased Opioid Agonists: 3-Hydroxy-N-Phenethyl-5-Phenylmorphans with Three-Carbon Chain Substituents at C9
E. Gutman, E. Bow, F. Li, A. Sulima, S. Kaska, R. Crowley, T. Prisinzano, Y. S. Lee, S. A. Hassan, G. Imler, J. Deschamps, A. Jacobson, and K. C. Rice; RSC Med. Chem. 11, 896 (2020)

The Intriguing Effects of Substituents in the N-Phenethyl Moiety of Norhydromorphone: A Bifunctional Opioid from a Set of "Tail Wags Dog" Experiments
M. Wang, T. C. Irvin, C. A. Herdman, R. D. Hanna, S. A. Hassan, Y. S. Lee, S. Kaska, R. S. Crowly, T. Prisinzano, S. L. Whithey, C. A. Paronis, J. Bergman, S. Inan, E. B. Geller, M. W. Adler, T. A. Kopajtic, J. L. Katz, A. M. Chadderdon, J. R. Traynor, A. E. Jacobson, and K. C. Rice; Molecules 25, 2640 (2020)

Artificial Neural Networks for the Inverse Design of Nanoparticles with Preferential Nano-Bio Behaviors
S. A. Hassan; J. Chem. Phys. 153, 054102 (2020)

A Point Mutation in the Nuclease Domain of MLH3 Eliminates Repeat Expansions in a Mouse Stem Cell Model of the Fragile X-Related Disorders
B. E. Hayward, P. J. Steinbach, and K. Usdin; Nucleic Acids Res. 48, 7856 (2020)

Nanosecond Timescale Dynamics and Conformational Heterogeneity in Human Glucokinase Regulation and Disease
S.M. Sternisha, A.C. Whittington, J.A. Martinez Fiesco, C. Porter, M.M. McCray, T. Logan, C. Olivieri, G. Veglia, P.J. Steinbach, and B.G. Miller; Biophys. J. 118, 1109 (2020)

HLA and Autoantibodies Define Scleroderma Subtypes and Risk in African and European Americans and Suggest a Role for Molecular Mimicry
P. Gourh, S.A. Safran, T. Alexander, S.E. Boyden, N.D. Morgan, A.A. Shah, M.D. Mayes, A. Doumatey, A.R. Bentley, D. Shriner, R.T. Domsic, T.A. Medsger Jr., P.S. Ramos, R.M. Silver, V.D. Steen, J. Varga, V. Hsu, L.A. Saketkoo, E. Schiopu, D. Khanna, J.K. Gordon, B. Kron, L.A. Criswell, H. Gladue, C.T. Derk, E.J. Bernstein, S.L. Bridges Jr., V.K. Shanmugam, K.D. Kolstad, L. Chung, S. Kafaja, R. Jan, M. Trojanowski, A. Goldberg, B.D. Korman, P.J. Steinbach, S.C. Chandrasekharappa, J.C. Mullikin, A. Adeyemo, C. Rotimi, F.M. Wigley, D.L. Kastner, F. Boin, and E.F. Remmers; Proc. Natl. Acad. Sci. USA 117, 562 (2020)

Establishment of an In Vitro RNA Polymerase Transcription System: A New Tool to Study Transcriptional Activation in Borrelia burgdorferi
W. K. Boyle, L. S. Hall, A. A. Armstrong, D. P. Dulebohn, D. S. Samuels, F. C. Gherardini, and T. J. Bourret; Sci. Rep. 10, 8246 (2020)

Accommodation of In-Register N-Linked Glycans on Prion Protein Amyloid Cores
E. Artikis, A. Roy, H. Verli, Y. Cordeiro, and B. Caughey; ACS Chem. Neurosci. 11, 4092 (2020)

Comparison of Solution Properties of Polymethylated Lanthanide Complexes with Opposite Chirality of the Pendant Arms
A. C. Opina, M. Strickland, Y. S. Lee, N. Tjandra, R. Swenson, and O. Vasalatiy; Inorg. Chem. 58, 15788 (2019)

Strong Dependence of the Nano-Bio Interactions on Core Morphology and Layer Composition of Ultrasmall Nanostructures
S. A. Hassan; J. Chem. Phys. 151, 105102 (2019)

Severe Autoinflammation in Four Patients with C-terminal Variants in Cell Division Control Protein 42 Homolog (CDC42) Successfully Treated with IL-1β Inhibition.
G. Yael, A. A. de Jesus, H. Alsaleem, C. Macaubas, A. Roy, D. Lovell, K. A. Jagadeesh, S. Alehashemi, L. Erdman, M. Grimley, and S. Talarico; J. Allergy Clin, Immunol. 144, 1122 (2019)

Development of R7BP Inhibitors through Cross-Linking Mass Spectrometry and Integrated Modeling
P. R. Adikaram, J.-H. Zhang, C. M. Kittock, M. Pandey, S. A. Hassan, N. G. Lue, G. Wang, M. Gucek, and W. F. Simonds; Commun. Biol. 2, 338 (2019)

Biallelic HEPHL1 Variants Impair Ferroxidase Activity and Cause an Abnormal Hair Phenotype
P. Sharma, M. Reichert, Y. Lu, T. C. Markello, D. R. Adams, P. J. Steinbach, B. Fuqua, X. Chepa-Lotrea, S. G. Kaler, C. D. Vulpe, G. J. Anderson, W. A. Gahl, and M. C. V. Malicdan; PLoS Genet. 15, 1008143 (2019)

Characterization of the Phosphorylation Site of GRTH/DDX25 and Protein Kinase A Binding Interface Provides Structural Basis for the Design of a Non-Hormonal Male Contraceptive
M. Raju, S. A. Hassan, R. Kavarthapu, R. Anbazhagan, and M. L. Dufau; Sci. Rep. 9, 6705 (2019)

Synthesis and Evaluation of Two New Candidate High-affinity Full Agonist PET Radioligands for Imaging 5-HT1B Receptors
A. Lindberg, S. Lu, S. Nag, M. Schou, J. S. Liow, S. S. Zoghbi, M. P. Frankland, R. L. Gladding, C. L. Morse, A. Takano, N. Amini, C. S. Elmore, Y. S. Lee, R. B. Innis, C. Halldin, and V. W. Pike;
Nuclear Med. Bio. 70, 1 (2019)

** Tetrahydroxamate Chelators of Zirconium89 and Niobium90 for use in Diagnostic Applications
F. Guerard, Y. S. Lee, and M. W. Brechbiel; U.S. Patent No. 10137212 (granted on Nov. 27, 2018)

GATA2 Deficiency and Human Hematopoietic Development Modelled using Induced Pluripotent Stem Cells
M. Jung, S. Cordes, J. Zou, S. J. Yu, X. Guitart, S. G. Hong, V. Dang, E. Kang, F. S. Donaires, S. A. Hassan, A. P. Hsu, S. M. Holland, D. D. Hickstein, D. Townsley, C. E. Dubnar, and T. Winkler;
Blood Adv. 2, 3553 (2018)

Modeling the Assembly Order of Multimeric Heteroprotein Complexes
L. X. Peterson, Y. Togawa, J. Esquivel-Rodriguez, G. Terashi, C. Christoffer, A. Roy, W. Shin, and D. Kihara; PLoS Comput. Biol. 14, e1005937 (2018)

Entropic Allostery Dominates the Phosphorylation‐dependent Regulation of Syk Tyrosine Kinase Release from Immunoreceptor Tyrosine‐based Activation Motifs
F. Chao, A. Roy, and C. B. Post; Protein Sci. 27, 1780 (2018)

Self-Adaptive Multiscaling Algorithm for Efficient Simulations of Many-Protein Systems in Crowded Conditions
S. A. Hassan; Phys. Chem. Chem. Phys. 20, 28544 (2018)

Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model
P. J. Steinbach; J. Phys. Chem. B 122, 11355 (2018)

Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements
M. Connolly, A. Arra, V. Zvoda, P. J. Steinbach, P. A. Rice, and A. Ansari; J. Phys. Chem. B 122, 11519 (2018)

Loss of Function Mutations in VARS Encoding Cytoplasmic Valyl-tRNA Synthetase Cause Microcephaly, Seizures and Progressive Cerebral Atrophy
J. Stephen, S. Nampoothiri, A. Banerjee, N. J. Tolman, J. M. Penninger, U. Elling, C. A. Agu, J. D. Burke, K. Devadathan, R. Kannan, Y. Huang, P. J. Steinbach, S. A. Martinis, W. A. Gahl, and M. C. V. Malicdan;
Human Genet. 137, 293 (2018)

Enhanced Spontaneous DNA Twisting/Bending Fluctuations Unveiled by Fluorescence Lifetime Distributions Promote Mismatch Recognition by the Rad4 Nucleotide-Excision-Repair Complex
S. Chakraborty, P. J. Steinbach, D. Paul, H. Mu, S. Broyde, J.-H. Min, and A. Ansari; Nucleic Acids Res. 46, 1240 (2018)

Binding Kinetics of Ultrasmall Gold Nanoparticles with Proteins
A. Lira, R. Ferreira, R. Torquato, K. Riske, H. Zhao, M. Oliva, S. A. Hassan, P. Schuck, and A. A. Sousa; Nanoscale 10, 3235 (2018)

Bifunctional Aryliodonium Salts for Highly Efficient Radioiodination and Astatination of Antibodies
F. Guerard, L. Navarro, Y. S. Lee, C. Alliot, M. Cherel, M. W. Brechbiel, and J. F. Gestina; Bioorg. Med. Chem. 25, 5975 (2017)

* In Silico Approaches to Structure and Function of Cell Components and their Assemblies: Molecular Electrostatics and Solvent Effects
S. A. Hassan and E. L. Mehler; in Comprehensive Biophysics, expanded and revised for the Reference Module in Life Science, Elsevier (2017)

Computational Study of the Forces Driving Aggregation of Ultrasmall Nanoparticles in Biological Fluids
S. A. Hassan; ACS Nano 11, 4145 (2017)

Modeling Disordered Protein Interactions from Biophysical Principles
L. X. Peterson, A. Roy, C. Christoffer, G. Terashi, and D. Kihara; PLoS Comput. Biol. 13, e1005485 (2017)

Human and Server Docking Prediction for CAPRI Round 30‐35 using LZerD with Combined Scoring Functions
L. X. Peterson, H. Kim, J. Esquivel‐Rodriguez, A. Roy, X. Han, W. Shin, J. Zhang, G. Terashi, M. Lee, and D. Kihara; Proteins 85, 513 (2017)

HLA-DQ β1 Alleles Associated with Epstein-Barr Virus (EBV) Infectivity and EBV gp42 Binding to Cells
Q. Li, W. Bu, E. Gabriel, F. Aguilar, Y. Hoshino, H. Miyadera, C. Hess, R. L. Hornung, A. Roy, and J. I. Cohen; JCI Insight 2, e85687 (2017)

Modulation of Opioid Receptor Affinity and Efficacy via N-Substitution of 9b-hydroxy-5-(3-hydroxyphenyl)morphan: Synthesis and Computer Simulation Study
P. M. Truong, S. A. Hassan, Y. S. Lee, T. A. Kopajtic, J. L. Katz, A. M. Chadderdon, J. R. Traynor, J. R. Deschamps, A. R. Jacobson, and K. C. Rice; Bioorg. Med. Chem. 25, 2406 (2017)

Investigation of the Complexation of natZr(IV) and 89Zr(IV) by Hydroxypyridinones for the Development of Chelators for PET Imaging Applications
F. Guerard, M. Beyler, Y. S. Lee, R. Tripier, J. F. Gestin, and M. W. Brechbiel; Dalton Trans. 46, 4749 (2017)

Crystal Structure of Diaryliodonium Fluorides and their Implications for Fluorination Mechanisms
Y. S. Lee, J. H. Chun, M. Hodoscek, and V. W. Pike; Chem. Eur. J. 23, 4353 (2017)

CELSR2, Encoding a Planar Cell Polarity Protein, is a Putative Gene in Joubert Syndrome with Cortical Heterotopia, Microophthalmia and Growth Hormone Deficiency
T. Vilboux, M. C. V. Malicdan, J. C. Roney, A. R. Cullinane, J. Stephen, D. Yildirimli, J. Bryant, R. Fischer, M. Vemulapalli, J. C. Mullikin, NISC Comparative Sequencing Program, P. J. Steinbach, W. A. Gahl, M. Gunay-Aygun; Am. J. Med. Genet. Part A 173, 661 (2017)

Cytoskeletal Abnormalities and Neutrophil Dysfunction in WDR1 Deficiency
D. B. Kuhns, D. M. Fink, U. Choi, C. Sweeney, K. Lau, D. L. Priel, D. Riva, L. Mendez, G. Uzel, A. F. Freeman, K. N. Olivier, V. L. Anderson, R. Currens, V. Mackley, A. Kang, M. Adeli, E. Mace, J. S. Orange, E. Kang, S. J. Lockett, D. Chen, P. J. Steinbach, A. P. Hsu, K. A. Zarember, H. L. Malech, J. I. Gallin, and S. M. Holland; Blood 128, 2135 (2016)

Computational Study of the Inhibitory Mechanism of Kinase CDK5 Hyperactivity by Peptide p5 and Derivation of a Pharmacophore
A. Cardone, M. Brady, R. Sriram, H. C. Pant, and S. A. Hassan; J. Comput. Aided Mol. Des. 30, 513 (2016)

Unexpected Behavior of the Heaviest Halogen Astatine in the Nucleophilic Substitution of Aryliodonium Salts
F. Guerard, Y. S. Lee, K. Baidoo, J.-F. Gestin, and M. W. Brechbiel; Chem. Eur. J. 22, 12205 (2016)
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Biointeractions of Ultrasmall Glutathione-coated Gold Nanoparticles: Effect of Small Size Variations
A. A. Sousa, S. A. Hassan, L. L. Knittel, A. Balbo, M. A. Aronova, P. H. Brown, P. Schuck, and R. D. Leapman; Nanoscale 8, 6577 (2016)

Analysis of the Isomer Ratios of Polymethylated-DOTA Complexes and the Implications on Protein Structural Studies.
A. C. Opina, M. Strickland, Y. S. Lee, N. Tjandra, R. A. Byrd, R. E. Swenson, and O. Vasalatiy; Dalton. Trans. 45, 4673 (2016)

An Investigation of (Diacetoxyiodo)arenes as Precursors for Preparing No-Carrier-Added [18F]Fluoroarenes fromCyclotron-Produced [18F]Fluoride Ion.
M. B. Haskali, S. Telu, Y. S. Lee, C. L. Morse, S. Lu, and V. W. Pike; J. Org. Chem. 81, 297 (2016)

Structural Basis of Species-dependent Differential Affinity of 6-Alkoxy-5-aryl-3-pyridinecarboxamide Cannabinoid Receptor 1 Antagonists
M. R. Iyer, R. Cinar, J. Liu, G. Godlewski, G. Szanda, H. Puhl, S. R. Ikeda, J. Deschamps, Y. S. Lee, P. J. Steinbach, and G. Kunos; Mol. Pharmacol. 88, 238 (2015)

Detection and Characterization of Nonspecific, Sparsely-populated Binding Modes in the Early Stages of Complexation
A. Cardone, A. Bornstein, H. C. Pant, M. Brady, R. Sriram, S. A. Hassan; J. Comp. Chem. 36, 983 (2015)

Role of Albumin in the Formation and Stabilization of Nanoparticle Aggregates in Serum Studied by Continuous Photon Correlation Spectroscopy and Multiscale Computer Simulations
A. Bhirde, S. A. Hassan, E. Harr, and X. Chen; J. Phys. Chem. C 118, 16199 (2014)

Implicit Treatment of Solvent Dispersion Forces in Protein Simulations
S. A. Hassan; J. Comput. Chem. 35, 1621 (2014)

Impact of subdomain D1 of the short form S1b of the human prolactin receptor on its inhibitory action on the function of the long form of the receptor induced by prolactin
J. H. Kang, S. A. Hassan, P. Zhao, C. H. Tsai-Morris, and M. L. Dufau; Biochim. Biophys. Acta 1840, 2272 (2014)

** Zirconium-89 PET Imaging Agent for Cancer
F. Guerard, Y. S. Lee, and M. W. Brechbiel; U.S. Patent Application No. 61/779016

Rational Design, Synthesis, and Evaluation of Tetrahydroxamic Acid Chelators for Stable Complexation of Zirconium(IV)
F. Guerard, Y. S. Lee, and M. W. Brechbiel; Chem. Eur. J. 20, 5584 (2014)

Drastic neofunctionalization associated with evolution of the timezyme AANAT 500 Mya
J. Falcon, S. L. Coon, L. Besseau, D. Cazamea-Catalan, M. Fuentes, E. Magnanou, C.-H. Paulin, G. Boeuf, S. Sauzet, E. H. Jorgensen, S. Mazan, Y. I. Wolf, E. V. Koonin, P. J. Steinbach, S. Hyodo, and D. C. Klein; Proc. Natl. Acad. Sci. USA 111, 314 (2014)

Specific and Non-Specific Protein Association in Solution: Computation of Solvent Effects and Prediction of First-Encounter Modes for Efficient Configurational-Bias Monte Carlo Simulations
A. Cardone, H. Pant, and S. A. Hassan; J. Phys. Chem. B 117, 12360 (2013)

** Zirconium-89 PET Imaging Agent for Cancer
F. Guerard, Y. S. Lee, and M. W. Brechbiel; Foreign, PCT Patent Application No. PCT/US2014/24048

Investigation of Zr(IV) and 89Zr(IV) complexation with hydroxamates: progress towards designing a better chelator than desferrioxamine B immuno-PET imaging
F. Guerard, Y. S. Lee, R. Tripier, L. P. Szajek, J. R. Deschamps, and M. W. Brechbiel; Chem. Commun. 49, 1002 (2013)

Z and E rotamers of N-formyl-1-bromo-4-hydroxy-3-methoxy-morphinan-6-one and their intercoversion studied by 1H/13C NMR spectroscopy and quantum chemical calculations
A. Sulima A, K. Cheng, A. E. Jacobson, K. Rice, K. Gawrisch, and Y. S. Lee; Magn. Reson. Chem. 51, 82 (2013)

Self-consistent Treatment of the Local Dielectric Permittivity and Electrostatic Potential in Solution for Polarizable Macromolecular Force Fields
S. A. Hassan; J. Chem. Phys. 137, 7 (2012)

Identifying Protein Kinase Target Preferences using Mass Spectrometry
J. Douglass, R. Gunaratne, D. Bradford, F. Saeed, J. D. Hoffert, P. J. Steinbach, M. A. Knepper, and T. Pisitkun; Am. J. Physiol. Cell Physiol. 303, C715 (2012)

Molecular and Biochemical Characterization of a Unique Mutation in CCS, the Human Copper Chaperone to Superoxide Dismutase
P. Huppke, C. Brendel, G. C. Korenke, I. Marquardt, A. Donsante, L. Yi, J. D. Hicks, P. J. Steinbach, C. Wilson, O. Elpeleg, L. B. Moller, J. Christodoulou, S. G. Kaler, and J. Gartner; Human Mutation 33, 1207 (2012)

Filtering Artifacts from Lifetime Distributions when Maximizing Entropy using a Bootstrapped Model
P. J. Steinbach; Anal. Biochem. 427, 102 (2012)

Solution Structures of the Prototypical 18 kDa Translocator Protein Ligand, PK 11195, elucidated with 1H/13C-NMR Spectroscopy and Quantum Chemistry
Y. S. Lee, F. G. Simeon, E. Briard, and V. W. Pike; ACS. Chem. Neurosci. 3, 325 (2012)

Probes for Narcotic receptor Mediated Phenomena. 44. Synthesis of an N-substituted 4-hydroxy-5-(3-hydroxyphenyl)morphan with High Affinity and Selective Antaginist Activity
M. R. Iyer, Y. S. Lee, J. R. Deschamps, C. M. Dersch, R. B. Rothman, A. E. Jacobson, and K. C. Rice; Eur. J. Med. Chem. 50, 44 (2012)

Structure of Ddn, the Deazaflavin-dependent Nitroreductase from Mycobacterium Tuberculosis involved in Bioreductive Activation of PA-824
S. E. Cellitti, J. Shaffer, D. H. Jones, T. Mukherjee, M. Gurumurthy, B. Bursulaya, H. I. Boshoff, I. Choi, A. Nayyar, Y. S. Lee, J. Cherian, P. Niyomrattanakit, T. Dick, U. H. Manjunatha, C. E. Barry III, G. Spraggon, and B. H. Geierstanger; Structure 20, 101 (2012)

Substrate Specificity of the Deazaflavin-Dependent Nitroreductase (Ddn) from Mycobacterium Tuberculosis Responsible for the Bioreductive Activation of Bicyclic Nitroimidazoles
M. Gurumurthy, T. Mukherjee, C. S. Dowd, R. Singh, P. Niyomrattanakit, J. A. Tay, A. Nayyar, Y. S. Lee, J. Cherian, H. I. Boshoff, T. Dick, C. E. Barry III, and U. H. Manjunatha; FEBS Journal 279, 113 (2012)

* In Silico Approaches to Structure and Function of Cell Components and their Assemblies: Molecular Electrostatics and Solvent Effects
S. A. Hassan and E. L. Mehler; in Comprehensive Biophysics, Academic Press (2012)

Water-exclusion and Liquid-structure Forces in Implicit Solvation
S. A. Hassan and P. J. Steinbach; J. Phys. Chem. B 115, 14668 (2011)

Structure.Activity Relationships of Antitubercular Nitroimidazoles. 3. Exploration of the Linker and Lipophilic Tail of ((S)-2-Nitro-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazin-6-yl)-(4-trifluoromethoxybenzyl)amine (6-Amino PA-824)
J. Cherian et al.; J. Med. Chem. 54, 5639 (2011)

Probes for Narcotic Receptor Mediated Phenomena. 41. Unusual Inverse mu-agonists and Potent mu-opioid Antagoinists by Modification of the N-substituent in Enatiomeric 5-(3-hydroxyphenyl)morphans
K. Cheng, Y. S. Lee YS, R. B. Rothman, C. M. Dersch, R. W. Bittamn, A. E. Jacobson, and K. C. Rice; J.Med. Chem. 54, 957 (2011)

Microscopic Mechanism of Nanocrystal Formation from Solution by Cluster Aggregation and Coalescence
S. A. Hassan, J. Chem. Phys. 134, 114508 (2011)

Structural and Dynamic Determinants of Ligand Binding and Regulation of Cyclin-dependent Kinase 5 by Pathological Activator p25 and Inhibitory Peptide CIP
A. Cardone, S. A. Hassan, R. W. Albers, R. D. Sriram, and H. C. Pant; J. Mol. Biol. 401, 478 (2010)

Conformational Structure and Energetics of 2-methylphenyl(2'-methoxyphenyl)Iodonium Chloride: Evidence for Solution Clusters
Y. S. Lee, M. Hodoscek J. H. Chun, and V. W. Pike; Chem. E. J. 16, 10248 (2010)

Fast and High-Yield Microreactor Syntheses of ortho-Substituted [18F]Fluoroarenes from Reactions of [18F]Fluoride Ion with Diaryliodonium Salts
J. H. Chun, S. Liu, Y. S. Lee, and V. W. Pike; J. Org. Chem. 75, 3332 (2010)

Probes for Narcotic Receptor Mediated Phenomena. 40. N-substituted cis-4a-ethyl-1,2,3,4,4a,9a-hexahydrobenzofuro[2,3-c]pyridin-8-ols
M. R. Iyer, Y. S. Lee, J. R. Deschamps, R. B. Rothman, C. M. Dersch, A. E. Jacobson, and K. C. Rice; Bioorg. Med. Chem. 18, 91 (2010)

The Tensin-3 Protein, Including its SH2 Domain, is Phosphorylated by Src and Contributes to Tumorigenesis and Metastasis
X. Qian, G. Li, W. C. Vass, A. Papageorge, R. C. Walker, L. Asnaghi, P. J. Steinbach, G. Tosato, K. Hunter, and D. R. Lowy; Cancer Cell 16, 246 (2009)

Probes for Narcotic Receptor Mediated Phenomena. 39.1 Enantiomeric N-substituted Benzofurol[2,3-c]pyridin-6-ols: Synthesis and Topological Relationship to Oxide-bridged Phenylmorphans
Y. Zhang, Y. S. Lee, R. Rothman, C. Dersch, J. Deschamps, A. Jacobson, and K. Rice; J. Med. Chem. 52, 7570 (2009)

Transglutaminase-1 (TGM1) Gene Mutations in Autosomal Recessive Congenital Ichthyosis: Summary of Mutations (Including 23 Novel) and Modeling of TGase-1
M. L. Herman, S. Farasat, P. J. Steinbach, M. H. Wei, O. Toure, P. Fleckman, P. Blake, S. J. Bale, J. R. Toro; Human Mutation 30, 537 (2009)

Intramolecular Disulfide Bridges of the Prolactin Receptor Short Form are required for its Inhibitory Action on the Function of the Long Form of the Receptor
Y. L. Xie, S. A. Hassan, A. M. Qazi, C. H. Tsai-Morris, and M. L. Dufau; Mol. Cell. Biol. 29, 2546 (2009)

* Modeling Aqueous Solvent Effects through Local Properties of Water
S. A. Hassan and E. L. Mehler; in Modeling Solvent Environments, Ed. M. Feig, Wiley-VCH (2009)

Morphology of Ion Clusters in Aqueous Electrolytes
S. A. Hassan; Phys. Rev. E 77, 031501 (2008)

Evidence that Proline Focuses Movement of the Floppy Loop of Arylalkylamine N-Acetyltransferase
J. Pavlicek, S. L. Coon, S. Ganguly, J. Weller, S. A. Hassan, D. L. Sackett, and D. C. Klein; J. Biol. Chem. 283, 14552 (2008)

Computer Simulation of Ion Cluster Speciation in Concentrated Aqueous Solutions at Ambient Conditions
S. A. Hassan; J. Phys. Chem. B 112, 10573 (2008)

Design of Drug-Resistant Alleles of Type-III Phosphatidylinositol 4-Kinases using Mutagenesis and Molecular Modeling
A. Balla, G. Tuymetova, B. Toth, Z. Szentpetery, X. Zhao, Z. A. Knight, K. Shokat, P. J. Steinbach, and T. Balla; Biochemistry 47, 1599 (2008)

Identification of the Transition States in the Inversion of 1,4-Benzodiazepines with the Ab-Initio Replica Path Method
Y. S. Lee, V. W. Pike, M. Hodoscek; J. Phys. Chem. A 112, 1604 (2008)

Synthesis and Pharmacological Effects of the Enantiomers of the N-phenethyl Analogues of the Ortho and Para e- and f-oxide-bridged Phenylmorphans
J. Zezula, L. B. Singer, A. K. Przybyl, A. Hashimoto, C. M. Dersch, R. B. Rothman, J. R. Deschamps, Y. S. Lee, A. E. Jacobson, K. C. Rice; Org. Biomol. Chem. 6, 2868 (2008)

Probes for Narcotic Receptor Mediated Phenomena. 37. Synthesis and Opioid Binding Affinity of the Final Pair of Oxide-bridged Phenylmorphans, rac-(4R,6aS,11bR)-3-Methyl-2,3,4,5,6,6a-hexahydro-1H-4,11b-methanobenzofuro[3,2-d]azocine-8-ol and -10-ol, the ortho-b and para-b Isomers and their N-Phenethyl Analogs
M. Kurimura, H. Liu, A. Sulima, A. Hashimoto, A. K. Przybyl, J. R. Deschamps, C. M. Dersch, R. B. Rothman, Y. S. Lee, A. E. Jacobson, K. C Rice; J. Med. Chem. 51, 7866 (2008)

Targeted Deletion in the beta20-beta21 Loop of HIV Envelope Glycoprotein gp120 Exposes the CD4 Binding Site for Antibody Binding
I. Berkower, C. Patel, Y. Ni, K. Virnik, Z. Xiang, and A. Spadacini; Virology 377, 330 (2008)

Liquid-Structure Forces and Electrostatic Modulation of Biomolecular Interactions in Solution
S. A. Hassan; J. Phys. Chem. B 111, 227 (2007)

Prediction of Side-Chain Conformations on Protein Surfaces
Z. Xiang, P. J. Steinbach, M. P. Jacobson, R. A. Friesner, and B. Honig; Proteins 66, 814 (2007)

Probes for Narcotic Receptor Mediated Phenomena. 34. Synthesis and Structure-Activity Relationships of a Potent mu-Agonist gamma-Antagonist and an Exceedingly Potent Antinociceptive in the Enantiomeric C9-Substituted 5-(3-Hydroxyphenyl)-N-phenylethylmorphan Series
A. C. Hiebel, Y. S. Lee, E. Bilsky, D. Giuvelis, J. R. Deschamps, D. A. Parrish, M. D. Aceto, E. L. May, L. S. Harris, A. Coop, A. E. Jacobson, K. C. Rice; J. Med. Chem. 50, 3765 (2007)

Loss of Hsp90 Association up-Regulates Src-dependent ErbB2 Activity
W. Xu, X. Yuan, K. Beebe, Z. Xiang, and L. Neckers; Mol. Cell. Biol. 27, 220 (2007)

Ab initio Computer Modeling of Loops in G-protein Coupled Receptors: Lessons from the Crystal Structure of Rhodopsin
E. L. Mehler, S. A. Hassan, S. Kortagere, and H. Weinstein; Proteins 64, 673 (2006)

Effects of Electric Fields on Proton Transport through Water Chains
S. A. Hassan, G. Hummer, and Y. S. Lee; J. Chem. Phys. 124, 204510 (2006)

Biological Effect of a Novel Mutation in the Third Leucine-Rich Repeat of Human Luteinizing Hormone Receptor
M. Y. K. Leung, P. J. Steinbach, D. Bear, V. Baxendale, P.Y. Fechner, O. M. Rennert, and W. Y. Chan; Mol. Endocrinol. 20, 2493 (2006)

Fumarate Hydratase Enzyme Activity in Lymphoblastoid Cells and Fibroblasts of Individuals in Families with Hereditary Leiomyomatosis and Renal Cell Cancer
M. Pithukpakorn, M. H. Wei, O. Toure, P. J. Steinbach, G. M. Glenn, B. Zbar, W. M. Linehan, and J. R. Toro; J. Med. Genet. 43, 755 (2006)

* Advances in Homology Protein Structure Modeling
Z. Xiang; Curr. Prot. Pept. Sci. 7, 217 (2006)

* Computer Simulations of Protein-Ligand Interaction: Challenges and Applications
S. A. Hassan, L. Gracia, G. Vasudevan, and P. J. Steinbach; in Methods in Molecular Biology, Ed. U. Nienhaus, Humana Press (2005)

Long Dynamics Simulations of Proteins using Atomistic Force fields and a Continuum Representation of Solvent Effects: Calculation of Structural and Dynamic Properties
X. Li, S. A. Hassan and E. L. Mehler; Proteins 60, 464 (2005)

From Quantum Chemistry and the Classical Theory of Polar Liquids to Continuum Approximations in Molecular Mechanics Calculations
S. A. Hassan and E. L. Mehler; Int. J. Quantum Chem. 102, 986 (2005)

Amino Acid Side Chain Interactions in the Presence of Salts
S. A. Hassan; J. Phys. Chem. B 109, 21989 (2005)

Eucharyotic Ribonucleases H1 Act Processively by Interactions through the Duplex RNA-binding Domain
S. A. Gaidamakov, I. I. Gorshkova, P. Schuck, P. J. Steinbach, H. Yamada, S. M. Cerritelli, and R. J. Crouch; Nucl. Acids Res. 33, 2166 (2005)

Polyproline and the Spectroscopic Ruler Revisited with Single-Molecule Fluorescence
B. Schuler, E. A. Lipman, P. J. Steinbach, M. Kumke, and W. A. Eaton; Proc. Natl. Acad. Sci. USA 102, 2754 (2005)

Surface Charge and Hydrophobicity determine ErbB2 binding to the HSP90 Chaperone Complex
W. Xu, X. Yuan, Z. Xiang, E. Mimmaugh, M. Marcu, and L. Neckers; Nature Struct. Mol. Biol. 12, 120 (2005)

Mechanistic Hypotheses of Structure-Function Relations of Integrin aIIb3 based on a Refined Three-Dimensional Model
M. Filizola, S. A. Hassan, A. Artoni, B. S. Coller, and H. Weinstein; J. Biol. Chem. 279, 24624 (2004)

Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium
S. A. Hassan; J. Phys. Chem. B 108, 19501 (2004)

Exploring Peptide Energy Landscapes: A Test of Force Fields and Implicit Solvent Models
P. J. Steinbach; Proteins 57, 665 (2004)

Mutation in the Leucine-rich Repeat C-flanking Region of Platelet Glycoprotein Ib-beta Impairs Assembly of von Willebrand Factor Receptor
J. Tang, S. Stern-Nezer, P. C. Liu, L. Matyakhina, M. Riordan, N. L. C. Luban, P. J. Steinbach and S. G. Kaler; Thromb. Haemost. 92, 75 (2004)

Dynamics of Proton Transfer in Bacteriorhodopsin
Y. S. Lee and M. Krauss; J. Am. Chem. Soc. 126, 2225 (2004)

Quantum Chemical Calculations and Mutational Analysis Suggest Heat Shock Protein 90 Catalyzes Trans-Cis Isomerization of Geldanamycin
Y. S. Lee, M. G. Marcu and L. Neckers; Chem. Biol. 11, 991 (2004)

Structure and Reaction in the Active Site of Mammalian Adenylyl Cyclase
Y. S. Lee and M. Krauss; J. Phys. Chem. B 108, 4508 (2004)

Reversible Proton Transfer Dynamics in Bacteriorhodopsin
Y. S. Lee and M. Krauss; J. Mol. Struct. 700, 243 (2004)

* The Rules of Attraction
L. Neckers and Y. S. Lee; Nature 106, 357 (2003)

Exploring the QM/MM Replica Method: A Pathway Optimization of the Chorismate to Prephenate Claisen Rearrangement Catalyzed by Chorismate Mutase
H. L. Woodcock, M. Hodoscek, P. Sherwood, Y. S. Lee, H. F. Schafer III, and B. R. Brooks; Theor. Chem. Acc. 109, 140 (2003)

Hydrogen Bonding Interactions between Aldose Reductase Complexed with NADP(H) and Inhibitor Tolrestat Studied by Molecular Dynamics Simulations and Binding Assay
Y. S. Lee, M. Hodoscek, P. F. Kador, and K. Sugiyama; Chem-Biol Interact. 143, 307 (2003)