Selected Publications: (For a complete list, please visit Google Scholar)
-
Negi, S.S., Schein C.H., and Braun, W.,
The updated Structural Database of Allergenic Proteins (SDAP 2.0) provides 3D models for allergens and incorporated Bioinformatics Tools.
Journal of Allergy and Clinical Immunology: Global, Volume 2, Issue 4, November 2023, 100162.
Pubmed
Full Paper
- Lensink M, Brysbaert G, Raouraoua N, Bates P, Giulini M, Honorato RV, Noort Cv, Teixeira J, Bonvin AM, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy R, Wu T, Giri N, Quadir F, Chen C, Cheng J, Carpio CD, Ichiishi E, A LR, Fernández-Recio J, Harmalkar A, Chu L, Canner S, Smanta R, Gray J, Li H, Lin P, He J, Tao H, Huang S, Roel J, Jimenez-Garcia B, Christoffer C, J AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt J, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi S, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest J, Lee J, Pierce B, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, K KB, Lubecka E, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo J, Samsonov S, Slusarz R, Zieba K, Sieradzan A, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancuskas L, Dapkūnas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qiu L, Xu X, Zou X, Velankar S,Wodak JS.
Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment.
PROTEINS: Structure, Function, and Bioinformatics 2023. doi:10.22541/au.168888815.53957253/v1. PPR:PPR688537
Pubmed
Full Paper
-
Canon N, Schein CH, Braun W, Negi SS, Chen X, Kulis MD, Kim EH, Pathy V, Pozzoli M, Liu W, Dreskin SC.,
Alanine Scanning of the Unstructured Region of Ara h 2 and of a Related Mimotope Reveals Critical Amino Acids for IgE Binding.
Mol Nutr Food Res. 2023 Sep 14;e2300134. doi: 10.1002/mnfr.202300134.
Pubmed
Full Paper
-
Schein C.H., Rafael, G., Baker, W.S., Anaya, E.S., Schmidt, J.G., Weaver, S.C., Negi, S.S., and Braun, W.,
PCP consensus protein/peptide alphavirus antigens stimulate broad spectrum neutralizing antibodies.
Peptides, Volume 157, November 2022, 170844
Pubmed
-
Schein C.H., Negi, S.S., and Braun, W., Still SDAPing Along: 20 Years of the Structural Database of Allergenic Proteins. Front. Allergy 3:863172. doi: 10.3389/falgy.2022.863172
Full Paper
-
Negi, S.S., Schein C.H., and Braun, W., Regional and temporal coordinated mutation patterns in SARS-CoV-2 spike protein revealed by a clustering and network analysis
Scientific Reports. 12, Article number: 1128 (2022) Pubmed
-
Negi, S.S., Goldblum, R., Braun, W., and Horiuti, T.M., Design of peptides with high affinity binding to a monoclonal antibody as a basis for immunotherapy
Peptides. 145:170628, 2021 Pubmed
-
Schein C.H., McClellan, S.F., Levine, C.B., Negi, S.S., Braun, W.,Dreskin, S.C., Anaya,E.S., and Schmidt, J., Synthetic protein antigens for COVID-19 diagnostics
Peptides, 143:170583, 2021 Pubmed
-
Dreskin, S.C., Koppelman, S.J., Andorf, S., Nadeau, K.C., Kalra, A., Braun, W., Negi, S.S., Chen, X., Schein C.H., The importance of the 2S albumins for allergenicity and cross-reactivity of peanuts, tree nuts, and sesame seeds
Journal of Allergy and Clinical Immunology 147 (4), 1154-1163, 2021 Pubmed
-
Baker W.S., Negi S.S., Braun. W and Schein C.H, Producing physicochemical property consensus alphavirus protein antigens for broad spectrum vaccine design
Antiviral research 182, 104905, 2020 Pubmed
-
Dreskin S.C , Germinaro M., Reinhold D., Chen X., Vickery B.P., Kulis M., Burks W.A., Negi S.S., Braun W., Chambliss J.M., Eglite S. and McNulty C.MG, IgE binding to linear epitopes of Ara h 2 in peanut allergic preschool children undergoing oral Immunotherapy
Pediatric Allergy and Immunology 30 (8), 817-823, 2020 Pubmed
-
Kimble J.B., Malherbe D.C., Meyer M., Gunn B.M., Karim M.M., Ilinykh P.A., Iampietro M., Mohamed K.S., Negi S.S., Gilchuk P., Huang K., Wolf Y.I., Braun W., Crowe J.E. Jr, Alter G, Bukreyev A , Antibody-Mediated Protective Mechanisms Induced by a Trivalent Parainfluenza Virus-Vectored Ebolavirus Vaccine. Virol. 93 (4), 2019 Pubmed
-
Lu, W., Negi, S.S., Schein, C.H., Maleki, S.J., Hulburt, B.K. and Braun, W., Distinguishing allergens from non-allergenic homologues using Physical-Chemical Property (PCP) motifs, Molecular Immunology, 9, 1-8, 2018 Pubmed
-
Negi, S.S., Schein, C.H., Ladics, G., Mirsky, H., Chang, P., Rascle, J.B., Kough, J., Sterck, L., Papineni, S., Jez, J., Mouries, L., and Braun, W., Functional classification of protein toxins as a basis for bioinformatic screening, Scientific Reports, 7, 13940, 2017 Pubmed
-
Negi, S.S., and Braun, W., Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity, Bioinformatics, 33(7):1014-1020, 2017 Pubmed
-
Fongang, B., Kong, F., Negi, S.S., Braun, W. Kudlicki, A., A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes, Scientific Reports, 6, 35415, 2016 Pubmed
-
Chen, X.*, Negi, S.S.*, Liao, S., Gao, V., Braun, W., Dreskin, S.C. Conformational IgE epitopes of peanut allergens Ara h 2 and Ara h 6. Clin. Exp. Allergy, 46(8):1120-8, 2016 (*Equal contribution) Pubmed
-
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins, Sep;84 Suppl 1:323-48, 2016
Pubmed
-
Marceau, C.D., Negi, S.S., Hernandez, H., Callison, J, Marzi, A., Borisevich, V., Braun, W., Berry, J., Feldmann, H. and Rockx, B. Novel neutralizing monoclonal antibodies protect rodents against lethal filovirus challenges. Trials in Vaccinology, 3, 89-94, 2014
Pubmed
-
Bergren, N.A., Auguste, A.J., Forrester, N.L., Negi, S.S., Braun, W. and Weaver, S.C. Western equine encephalitis virus: evolutionary analysis of a declining alphavirus based on complete genome sequences. J. Virol., 88, 9260-9267, 2014
Pubmed
-
Navaratnarajah C.K., Negi, S.S., Braun, W. and Cattaneo, R. Membrane fusion triggering: three modules with different structure and function in the upper half of the measles virus attachment protein stalk. J. Biol. Chem., 287, 38543-38551, 2012
Pubmed
-
Sengupta, A.S, Negi, S.S., Leonard, V.H., Oezguen, N., Navaratnarajah, C.K., Braun, B. and Cattaneo, R. Base of the measles virus fusion trimer head receives the signal that triggers membrane fusion. J. Biol. Chem., 287, 33026-33035, 2012
Pubmed
-
Lu, W., Negi, S.S., Oberhauser, A.F. and Braun, W. Engineering proteins with enhanced mechanical stability by force-specific sequence motifs. Proteins, 80, 1308-1315, 2012
Pubmed
-
Tiwari, R.*, Negi, S.S.*, Braun, B., Braun, W., Pomes, A., Chapman, M.D., Goldblum, R.M. and Midoro-Horiuti, T. Validation of a phage display and computational algorithm by mapping a conformational epitope of Bla g 2. Int. Arch. Allergy Immunol., 157, 323-330, 2012 (*Equal contribution)
Pubmed
-
Negi, S.S. and Braun, W. Automated detection of conformational epitopes using phage display peptide sequences. Bioinform. Biol. Insights, 3, 71-81, 2009
Pubmed
-
Ivanciuc, O., Schein, C.H., Garcia, T.I., Oezguen, N., Negi, S.S. and Braun, W. Structural analysis of linear and conformational epitopes of allergens. Regul. Toxicol. Pharmacol., 54, S11-S19, 2009
Pubmed
-
Negi, S.S., Carol, A.A., Pandya, S., Braun, W. and Anderson, L.E. Co-localization of glyceraldehyde-3-phosphate dehydrogenase with ferredoxin-NADP reductase in pea leaf chloroplasts. J. Struct. Biol., 161, 18-30, 2008
Pubmed
-
Numan, O., Zhou, B., Negi, S.S., Ivanciuc, O., Schein, C.H., Labesse, G. and Braun, W. Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes. Mol. Immunol., 45, 3740-3747, 2008
Pubmed
-
Muralidhara, B.K., Ling, S., Negi, S.S. and Halpert, J.R. Thermodynamic fidelity of the mammalian cytochrome P450 2B4 active site in binding substrates and inhibitors. J. Mol. Biol., 377, 232-245, 2008
Pubmed
-
Negi, S.S., and Braun, W. Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces. J. Mol. Model., 13, 1157-1167, 2007
Pubmed
-
Muralidhara, B.K., Negi, S.S. and Halpert, J.R. Dissecting the thermodynamics and cooperativity of ligand binding in cytochrome P450 eryF. J. Am. Chem. Soc., 129, 2015-2024, 2007
Pubmed
-
Lokesh, R., Muralidhara, B.K., Negi, S.S. and Natarajan, A. Thermodynamics of phosphopeptide tethering to BRCT: The structural minima for inhibitor design. J. Am. Chem. Soc., 129, 10658-10659, 2007
Pubmed
-
Negi, S.S., Schein, C.H., Oezguen, N., Power, T.D. and Braun, W. InterProSurf: a web server for predicting interacting sites on protein surfaces. Bioinformatics, 23, 3397-3399, 2007
Pubmed
-
Kumar, S., Zhao, Y., Sun, L., Negi, S.S., Halpert, J.R. and Muralidhara, B.K. Rational engineering of human cytochrome P450 2B6 for enhanced expression and stability: importance of a Leu264Phe substitution. Mol. Pharmacol., 72, 1191-1199, 2007
Pubmed
-
Negi, S.S., Kolokoltsov, A.A., Schein, C.H., Davey, R.A. and Braun, W. Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus. J. Mol. Model, 12, 921-929, 2006
Pubmed
-
Muralidhara, B.K., Negi, S.S., Chin, C.C., Braun, W. and Halpert, J.R. Conformational flexibility of mammalian cytochrome P450 2B4 in binding imidazole inhibitors with different ring chemistry and side chains. Solution thermodynamics and molecular modeling. J. Biol. Chem., 281, 8051-8061, 2006
Pubmed