Welcome to Surendra's Research Page

Surendra Negi

Research Scientist II

Research Interests:

Bioinformatics and computational biology
Big data, predictive analytics and visual analytics for biomedical research
Molecular modeling, molecular docking and molecular dynamics simulation
Protein function prediction using evolutionary analysis and network analysis
Identification of hotspots on protein surfaces and their role in protein-protein interaction
Immunoinformatics for epitope discovery (B-cell and T-cell) and vaccine design
Computational approach for mosaic immunogen design
Prediction of cross-reactivity using conformational epitopes
In-silico methods for rapid screening of protein toxins
Computational analysis of protein allergenicity
Identification of potential drug targets
Human microbiome research
Deep machine learning methods (ML/AI) to understand protein function and protein-protein interactions

surendra.negi@gmail.com

ssnegi@utmb.edu

Teaching:

Computer Modeling of Macromolecular Structure and Function 2016 (Schedule_BMB_6206.docx ): Werner Braun and Surendra Negi
Course Description: The course BMB 6206 is a 15 week course with one 2h class every week. The course introduces the students to fundamental concepts of data representations, data formats and software tools for search, retrieval and analysis of amino acid and nucleotide sequences of genes and proteins, including recent developments of tools in systems biology and Next Generation Sequencing. Specific data bases discussed are gene and protein sequence databases, the Protein Data Bank of 3D protein structures and the SCOP and CATH databases of protein folds. The software tools include the BLAST, FASTA and Clustal W programs, computational methods for secondary and tertiary structure prediction of proteins, and methods for the analysis and validation of 3D structures.
The Computational Biology Facility is located in research building 6, 5th floor (map). Classes meet in the small Conference Room (5.416A).

Bioinformatics and Immunoinformatics Algorithms and Softwares:

Web server to predict functionally important amino acids on protein surface crucial for protein function and protein-protein interaction	InterProSurf
Web server to predict allergenicity using convolutional neural network (CNN) (allergenic potential of a protein)	AllergenPred
Web server to predict conformational epitopes on antigen protein using peptides selected from phage display experiments	EpiSearch
Web server to predict B-Cell epitope using antigen structure alone	BCEP
Web server for calculation of solvent accessible surface area of macromolecules	GetArea
Web server to predict cross-reactivity between allergenic proteins	Cross-React
Structure database of allergenic proteinss (SDAP)	SDAP
Web server to predict mutation profile of amino acids in SARS-CoV-2 protein	SARS-CoV-2
Homology Modeling Program	MPACK

Selected Publications: (For a complete list, please visit Google Scholar)

Yang, C., Negi, S.S., Schein C.H., Braun, W., and Kim, P., AllergenAI: a deep learning model predicting allergenicity based on protein sequence Submitted: bioRxiv, 2024 06.22.600179

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