| Category | Description |
|---|---|
| Bioinformatics & Computational Biology | Developing algorithms and tools to analyze biological data and simulate molecular systems |
| Big Data & Predictive Analytics | Applying machine learning and visual analytics to biomedical datasets for pattern discovery |
| Molecular Modeling & Simulation | Using molecular docking and dynamics to study protein-ligand interactions and structural behavior |
| Protein Function Prediction | Leveraging evolutionary and network-based analysis to predict protein roles and interactions |
| Protein-Protein Interaction Hotspots | Identifying surface hotspots critical for molecular interactions and binding specificity |
| Immunoinformatics & Epitope Discovery | Predicting B-cell and T-cell epitopes for vaccine design and immune profiling |
| Mosaic Immunogen Design | Computational design of mosaic antigens to enhance immune coverage and diversity |
| Cross-Reactivity Prediction | Modeling conformational epitopes to assess immune cross-reactivity and safety |
| Toxin Screening | Rapid in-silico identification and filtering of protein toxins for therapeutic safety |
| Allergenicity Analysis | Computational evaluation of protein allergenicity to support vaccine and drug development |
| Drug Target Identification | Discovering novel therapeutic targets using integrative structural and functional data |
| Human Microbiome Research | Studying host-microbiome interactions and microbial dynamics in health and disease |
| Deep Learning for Protein Analysis | Using ML/AI to model protein function and simulate complex protein-protein interactions |
| Malaria Parasite–Mosquito Protein–Protein Interactions | Studying molecular interactions between Plasmodium proteins and mosquito host receptors to understand transmission and identify intervention targets |
Instructors: Werner Braun and Surendra Negi
Course Format: 15-week course with one 2-hour class per week
Course Description:
This graduate-level course introduces students to fundamental concepts in computational biology, including data representations, formats, and software tools for the search, retrieval, and analysis of amino acid and nucleotide sequences. It covers systems biology and Next Generation Sequencing tools, and explores key databases such as the Protein Data Bank (PDB), SCOP, and CATH.
Students gain hands-on experience with bioinformatics tools including BLAST, FASTA, and Clustal W, and learn computational methods for predicting secondary and tertiary protein structures, as well as techniques for analyzing and validating 3D molecular models.
Location: Computational Biology Facility, Research Building 6, 5th Floor
Classroom: Small Conference Room (5.416A)
| Alogrithm/Software Name | Application | Link |
|---|---|---|
| InterProSurf | Predicts functionally important amino acids on protein surfaces for function and interaction | Visit |
| AllergenPred | Predicts allergenicity using convolutional neural networks (CNN) | Visit |
| AllergenAI | A deep learning model predicting allergenicity based on protein sequence | Visit |
| EpiSearch | Predicts conformational epitopes using phage display peptide data | Visit |
| BCEP | Predicts B-cell epitopes using antigen structure alone | Visit |
| GetArea | Calculates solvent-accessible surface area of macromolecules | Visit |
| Cross-React | Predicts cross-reactivity between allergenic proteins | Visit |
| SDAP | Structure database of allergenic proteins with integrated tools | Visit |
| SARS-CoV-2 Mutation Profiler | Predicts mutation profiles of amino acids in SARS-CoV-2 proteins | Visit |
| MPACK | Homology modeling program for generating 3D protein structures | Visit |
| Publication | Journal | Year | Links |
|---|---|---|---|
| Bernstein, J.S., Canon, N., Schein, C.H., Braun, W., Negi, S.S., et al. Fine resolution of the N-terminal IgE-binding epitope of Ara h 2: Discovery of variants with enhanced IgE binding. | J Allergy Clin Immunol | 2025 | PubMed |
| Yang, C., Negi, S.S., Schein, C.H., Braun, W., Kim, P. AllergenAI: a deep learning model predicting allergenicity based on protein sequence. | bioRxiv (Preprint) | 2024 | Preprint |
| Negi, S.S., Schein, C.H., Braun, W. The updated Structural Database of Allergenic Proteins (SDAP 2.0) provides 3D models for allergens and incorporated bioinformatics tools. | J Allergy Clin Immunol: Global | 2023 | PubMed |
| 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 | PubMed |
| 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 Ara h 2 and Mimotope Reveals Critical Amino Acids for IgE Binding. | Mol Nutr Food Res | 2023 | 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 alphavirus antigens stimulate broad spectrum neutralizing antibodies. | Peptides | 2022 | PubMed |
| Schein C.H., Negi, S.S., and Braun, W. Still SDAPing Along: 20 Years of SDAP. | Front. Allergy | 2022 | Full Paper |
| Negi SS, Schein CH, Braun W. Coordinated mutation patterns in SARS-CoV-2 spike protein. | Scientific Reports | 2022 | PubMed |
| Negi SS, Goldblum R, Braun W, Horiuti TM. Peptides for monoclonal antibody-based immunotherapy. | Peptides | 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 | 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 | J Allergy Clin Immunol | 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 | 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. | Pediatric Allergy Immunol | 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 | Virology | 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 | 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 | 2017 | PubMed |
| Negi, S.S., Braun, W. Cross-React: predicting allergen cross-reactivity. | Bioinformatics | 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 | 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 | 2016 | 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 | 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 | 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. | 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. | 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. | 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 | 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. (*Equal contribution). | Int. Arch. Allergy Immunol. | 2012 | PubMed |
| Negi, S.S., Braun, W. Automated detection of conformational epitopes. | Bioinform. Biol. Insights | 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. | 2009 | PubMed |
| Negi, S.S., Carol, A.A., Pandya, S., Braun, W., Anderson, L.E. Co-localization of glyceraldehyde-3-phosphate dehydrogenase with ferredoxin-NADP reductase in pea leaf chloroplasts. | J. Struct. Biol. | 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. | 2008 | PubMed |
| Muralidhara, B.K., Negi, S.S., Halpert, J.R. Thermodynamic fidelity of the mammalian cytochrome P450 2B4 active site in binding substrates and inhibitors | J. Mol. Biol. | 2008 | PubMed |
| Negi, S.S., Braun, W. Statistical analysis of physicochemical properties for protein interfaces. | J. Mol. Model. | 2007 | PubMed |
| Muralidhara, B.K., Negi, S.S., Halpert, J.R. Dissecting the thermodynamics and cooperativity of ligand binding in cytochrome P450 eryF | J. Am. Chem. Soc. | 2007 | PubMed |
| Lokesh, R., Muralidhara, B.K., Negi, S.S. and Natarajan. Thermodynamics of phosphopeptide tethering to BRCT: The structural minima for inhibitor design. | J. Am. Chem. Soc. | 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 | 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. | 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 | 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. | 2006 | PubMed |
🧬 Research Collaboration:
Some of the research areas described above present a considerable challenge, since structures of only a small fraction of protein complexes are known. Determination of co-crystal structures continues to be a demanding task. We have developed several computational and analytical methods to overcome these limitations and facilitate effective use of diverse experimental and clinical data.
🤝 Are interested in exploring a potential research collaboration?
Feel free to reach out via email:
surendra.negi@gmail.com or ssnegi@utmb.edu.
📍Disclaimer: This service is provided freely to the scientific community for the purpose of scientific research. There is no warranty for the service, either expressed or implied.