Yang, C., Negi, S.S., Schein C.H., Braun, W., and Kim, P.,
AllergenAI: a deep learning model predicting allergenicity based on protein sequence
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.M.G, IgE binding to linear epitopes of Ara h 2 in peanut allergic preschool children undergoing oral Immunotherapy
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.
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,
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,
Negi, S.S., and Braun, W., Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity,
Fongang, B.,
Kong, F., Negi, S.S., Braun, W. Kudlicki, A., A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes,
Chen, X.,
Negi SS, Liao S, Gao V, Braun W, Dreskin SC. Conformational IgE epitopes of peanut allergens Ara h 2 and Ara h 6
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 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. Lu, W., Negi, S.S., Oberhauser, A.F. and Braun,
W. Engineering proteins with enhanced mechanical
stability by force-specific sequence motifs. 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. Oezguen, N., Mantha, A.K., Izumi, T., Schein,
C.H., Mitra, S. and Braun,
W. MD simulation and experimental evidence for
Mg2+ binding at the b site in human AP endonuclease 1. Savidge, T.C., Urvil, P., Oezguen,
N., Ali, K., Choudhury, A., Acharya, V., Pinchuk, I., Torres, A.G.,
English, R.D., Wiktorowicz,
J.E., Loeffelholz, M.,
Kumar, R., Shi, L., Nie,
W., Braun, W., Herman, B., Hausladen,
A., Feng, H., Stamler, J.S.
and Pothoulakis, C.
Host S-nitrosylation
inhibits clostridial small
molecule-activated glucosylating
toxins. Ivanciuc, O., Gendel, S.M., Power, T.D.,
Schein, C.H. and Braun, W. AllerML:
Markup language for allergens. Navaratnarajah, C.K., Oezguen, N., Rupp, L., Kay, L.,
Leonard, V.H.J., Braun, W. and Cattaneo,
R. The heads of the measles virus attachment
protein move to transmit the fusion-triggering signal. Schein, C.H., Ivanciuc,
O., Midoro-Horiuti, T., Goldblum, R.M. and Braun,
W. An allergen portrait gallery: representative
structures and an overview of IgE
binding surfaces. Schein, C.H., Oezguen, N., van der Heden van Noort,
G.J., Filippov, D.V., Paul,
A., Kumar, E. and Braun, W. NMR solution structure
of poliovirus uridylyated
peptide linked to the genome (VPgpU). Negi, S.S. and Braun,
W. Automated Detection of Conformational Epitopes
using Phage Display Peptide Sequences. 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. Garcia, T.I., Oberhauser, A.F. and Braun,
W. Mechanical stability and differentially
conserved physical-chemical properties of Titin
Ig-domains. Ivanciuc, O., Midoro-Horiuti, T., Schein,
C.H., Xie, L., Hillman,
G.R., Goldblum, R.M. and
Braun, W. The property index PD predicts peptides
that cross-react with IgE
antibodies. Ivanciuc, O., Garcia,
T.I., Torres, M., Schein, C.H. and Braun, W.
Characteristic motifs for families of allergenic
proteins. Oezguen, N., 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. Oezguen, N., Kumar, S., Hindupur, A., Braun, W., Muralidhara, B.K. and Halpert, J.R.
Identification and analysis of conserved motifs in
cytochrome P450 family 2: Functional and structural role
of a Motif 187RFDYKD192 in CYP2B enzymes. Leonard, V.H.J., Sinn,
P.L., Hodge, G., Miest, T.,
Devaux, P., Oezguen, N., Braun, W., McCray,
P.B. Jr., McChesney, M.B.
and Cattaneo, R.
Measles virus blind to its epithelial cell receptor
remains virulent in rhesus monkeys but cannot cross the
airway epithelium and is not shed. Mantha, A.K., Oezguen, N., Bhakat, K.K., Izumi, T., Braun,
W. and Mitra, S.
Unusual Role of a Cysteine Residue in Substrate Binding
and Activity of Human AP-Endonuclease 1. Navaratnarajah, C.K., Vongpunsawad, S., Oezguen, N., Stehle, T., Braun, W.,
Hashiguchi, T., Maenaka,
K., Yanagi, Y. and Cattaneo, R. Dynamic
interaction of the measles virus hemagglutinin with its
receptor SLAM. Negi, S.S., Carol, A.,
Pandya, S., Braun, W. and Anderson, L.
Co-Localization of Glyceraldehyde-3-Phosphate
Dehydrogenase with Ferredoxin-NADP
Reductase in Pea Leaf Chloroplasts. Ivanciuc, O. and Braun,
W. Robust quantitative modeling of peptide binding
affinities for MHC molecules using physical-chemical
descriptors. Negi, S., Schein, C.H., Oezguen, N., Power, T.D. and
Braun, W. InterProSurf: a web server for
predicting interacting sites on protein surfaces. Negi, S. and Braun, W.
Statistical analysis of physical-chemical properties and
prediction of protein-protein interfaces. Oezguen, N., Schein, C.H., Peddi, S.R.,
Power, T.D., Izumi, T. and Braun, W. A
"moving metal mechanism" for substrate cleavage
by DNA repair endonuclease APE-1. Chen, D, Menche, G, Power, T.D.,
Peterson, J.W. and Schein, C.H .
Accounting for ligand-bound metal ions in docking small
molecules on adenylyl cyclase toxins. Schein, C.H. Ivanciuc O.
and Braun, W. Bioinformatics approaches to
classifying allergens and predicting cross-reactivity. Schein, C.H., Ivanciuc,
O. and Braun, W. Structural Database of Allergenic
Proteins (SDAP). 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. Schein, C.H., Oezguen, N., Volk, D.E., Garimella, R., Paul, A. and
Braun, W. NMR structure of the viral peptide linked to
the genome (VPg) of
poliovirus. Muralidhara, B.K., Negi., 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. Midoro-Horiuti, T., Schein, C.H.,
Mathura, V., Braun, W., Czerwinski, E.W., Togawa, A., Kondo, Y., Oka, T.,
Watanabe, M. and Goldblum,
R.M. Structural basis for epitope sharing between group
1 allergens of cedar pollen. Schein, C.H., Ivanciuc,
O. and Braun, W. Common physical-chemical properties
correlate with similar structure of the IgE epitopes of peanut
allergens. Schein, C.H., Zhou, B.
and Braun, W. Stereophysicochemical
variability plots highlight conserved antigenic areas in
Flaviviruses. von Messling,
V., Oezguen, N., Zheng, Q.,
Vongpunsawad, S., Braun, W.
and Cattaneo, R. Nearby
clusters of hemagglutinin residues sustain
SLAM-dependent canine distemper virus entry in
peripheral blood mononuclear cells. Cummins, S.F., Schein,
C.H., Xu, Y., Braun, W. and Nagle, G.T. Molluscan attractins,
a family of water-borne protein pheromones with
interspecific attractiveness. Schein, C.H., Zhou, B., Oezguen, N., Painter, S.D., Cummins,
S.F., Nichols, A.E., Akalal,
D.B.G., Schein, C.H., Braun, W., Smith, J.S., Susswein, A.J., Levy, M., de
Boer, P.A.C.M., ter Maat,
A., Miller, M.W., Scanlan,
C., Milberg, R.M., Sweedler,
J.V. and Nagle, G.T. Structural and functional
analysis of Aplysa attractins, a family of
water-borne protein phermones
with interspecific attractiveness. Ivanciuc, O., Oezguen, N., Izumi, T., Schein, C.H.,
Oezguen, N., Feng, Y. and
Braun, W. Effects of backbone contacts 3' to the abasic site on the cleavage and
the product binding by human apurinic/apyrimidinic endonuclease
(APE1). Vongpunsawad, S., Oezgun, N., Braun, W. and Cattaneo R. Selectively
receptor-blind measles viruses: identification of
residues necessary for SLAM- or CD46-induced fusion and
their localization on a new hemagglutinin structural
model. Midoro-Horiuti, T., Braun, W.
Developing computational tools for NMR: the early
days of protein NMR. Ivanciuc, O., Garimella, R., Xu, Y., Schein,
C.H., Rajarathnam, K.,
Painter, S.D., Nagle, G.T. and Braun, W. NMR
solution structure of attractin,
a water-borne protein pheromone from the mollusk Aplysia californica.
Schein, C.H., Ozgun, N., Izumi, T. and
Braun, W. Total sequence
decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic
endonucleases. Ivanciuc, O.I., Schein,
C.H. and Braun, W. Data
mining of sequences and 3D structures of allergenic
proteins. Hasan, R.J., Pawelczek, E., Urvil, P.T., Venkatarajan, M.S., Goluszko, P., Kur, J., Selvarangan, R., Nowicki, S., Braun, W. and Nowicki, B.J. Structure-function
analysis of decay-accelerating factor:
identification of residues important for binding of the
escherichia coli Dr adhesin and complement
regulation. Oezguen, N., Adamian, L., Xu, Y., Rajarathnam, K. and Braun,
W. Automated assignment and 3D structure
calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY
spectra. Venkatarajan, M.S. and Braun,
W. New quantitative descriptors of amino acids
based on multidimensional scaling of a large number of
physical-chemical properties. Soman ,K.V. and Braun,
W. Determining the 3D-fold of a protein
from approximate constraints: a simulation
study. Schein, C.H., Nagle,
G.T., Page, J., Sweedler, J.V., Xu, Y.,
Painter, S.D. and Braun, W. Aplysia
attractin: biophysical
characterization and modeling of a water-borne
pheromone. Williams, R.M., Obradovi. Z., Mathura, V.,
Braun, W., Garner, E.C., Young, J., Takayama, S., Brown, C.J.,
Dunker, A.K. The protein non-folding problem:
amino acid determinants of intrinsic order and
disorder. Soman , K.V., Schein,
C.H., Zhu, H. and Braun, W. Homology modeling and simulations of
nuclease structures. Xu, Y., Jablonsky, M.,
Jackson, P.L., Braun, W. and Krishna, N.R.
Automated assignment of NOESY cross peaks
and determination of the protein structure of a new
world scorpion neurotoxin using NOAH/DIAMOD. Zhu, H., Schein, C.H. and
Braun, W. MASIA: recognition of common
patterns and properties in multiple aligned protein
sequences. Bioinformatics 16(10):950-951,
2000. Soman, K.V.,
Midoro-Horiuti, T., Chu, J.Y., Goldblum, R.M., Brooks,
E.G., Braun, W. and Schein, C.H. Automated Homology modeling and characterization
of IgE binding epitopes
of mountain cedar allergen Jun a 3.
Submitted: bioRxiv, 2024.06. 22.600179
Abstract
Full Paper
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.
Abstract
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.
Abstract
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
Abstract
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.,
Peptide and protein alphavirus antigens for broad spectrum vaccine design
bioRxiv preprint doi: https://doi.org/10.1101/2022.05.26.493643
Abstract
Full Paper
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
Abstract
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)
Abstract
Full Paper
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
Abstract
Full Paper
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
Abstract
Full Paper
Read C.M, Plante, K., Rafael, G., Rossi, S.L., Braun, W., Weaver, S.C., and Schein C.H.,
Designing multivalent immunogens for alphavirus vaccine optimization
Virology, 561:117-124,2021
Abstract
Full Paper
Braun, B.A., Schein C.H., and Braun, W.,
D-graph clusters flaviviruses and B-coronaviruses according to their hosts, disease type and human cell receptors
Bioinform Biol Insights. 15. 2021
Abstract
Full Paper
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.
Abstract
Full Paper
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
Abstract
Full Paper
Pediatric Allergy and Immunology 30 (8), 817-823, 2020
Abstract
Full Paper
J Virol. 93 (4), 2019
Abstract
Full Paper
Molecular Immunology, 9, 1-8, 2018
Abstract
Full Paper
Scientific Reports, 7, 13940, 2017
Abstract
Full
Paper
Bioinformatics, 33(7):1014-1020, 2017
Abstract
Full
Paper
Scientific Reports, 6, 35415, 2016
Abstract
Full
Paper
Clin Exp Allergy. 2016 May 30. doi: 10.1111/cea.12764. [Epub ahead of print]
Abstract
Full
Paper
J. Virol., 4, JVI.01463-14, 2014.
Abstract
Full
Paper
Marceau, C.D., Negi, S.S., Hernandez, H., Callison, J., Marzi, A., Borisevich,
V., Braun, W., Berry, Jody., Feldmann,
H. and Rockx, B. Novel
neutralizing monoclonal antibodies protect rodents
against lethal filovirus
challenges
Trials in Vaccinology,
3, 89-94, 2014.
Abstract
Full
Paper
Rana, T., Hasan, R.J., Nowicki, S., Venkatarajan, M.S., Singh, R., Urvil, P.T., Popov, V., Braun,
W., Popik, W., Goodwin,
J.S. and Nowicki,
B.J. Complement Protective Epitopes and
CD55-Microtubule Complexes Facilitate the Invasion and
Intracellular Persistence of Uropathogenic
Escherichia coli.
J. Infec. Dis.,
209(7) 1066-1076, 2014 (Epub
Nov 20, 2013).
Abstract
Full
Paper
Braun, W. and Schein, C.H. Membrane Interaction
and Functional Plasticity of Inositol Polyphosphate
5-Phosphatases
Structure, 22(5), 664-666, 2014.
Abstract
Full
Paper
Power, T.D, Ivanciuc, O., Schein, C.H. and Braun,
W. Assessment of 3D models for allergen research.
PROTEINS: Struct. Funct. and
Bioinf., 81(4),
545-554, 2013.
Abstract
Full
Paper
J. Biol. Chem., 287(46), 38543-38551, 2012.
Abstract
Full
Paper
Apte-Sengupta, S., Negi,
S.S., Leonard, V.H.J., Oezguen,
N., Navaratnarajah, C.K.,
W. Braun, W. and Cattaneo,
R. Base of the measles virus fusion trimer head receives the signal
that triggers membrane fusion.
J. Biol. Chem., 287(39), 33026-33035, 2012.
Abstract
Full
Paper
Oezguen, N., Power, T.D., Urvil, P., Feng, H., Pothoulakis, C., Stamler, J.S., Braun, W. and Savidge, T.C. Clostridial toxins: Sensing a
target in a hostile gut environment.
Gut Microbes, 3(1), 35-41, 2012.
Abstract
Full
Paper
Proteins, 80(5), 1308-1315, 2012.
Abstract
Full
Paper
Int. Arch. Allergy Immunol.,
157(4), 323-330, 2012.
Abstract
Full
Paper
Bioinformation, 7(4),
184-198, 2011.
Abstract
Full
Paper
Nat. Med., 17(9), 1136-1142, 2011.
Abstract
Full
Paper
Regul. Toxicol. Pharmacol.,
60(1), 151-160, 2011.
Abstract
Full
Paper
Nat. Struct. Mol. Biol.,
18(2), 128-134, 2011.
Abstract
Full
Paper
Bioinform. Biol.
Insights, 4, 113-125, 2010.
Abstract
Full
Paper
Peptides, 31(8), 1441-1448, 2010.
Abstract
Full
Paper
Bioinform. Biol.
Insights, 3,
71-81, 2009.
Abstract
Full
Paper
Regul. Toxicol. Pharmacol.,
54(3 Suppl), S11-S19, 2009.
Abstract
Full
Paper
PROTEINS: Struct. Funct. and
Bioinf., 75(3),
706-718, 2009.
Abstract
Full
Paper
Mol. Immunol.,
46(5), 873-883, 2009.
Abstract
Full
Paper
Mol. Immunol.,
46(4), 559-568, 2009.
Abstract
Full
Paper
Mol. Immunol.,
45(14), 3740-3747, 2008.
Abstract
Full
Paper
J. Biol. Chem., 283(31), 21808-21816, 2008.
Abstract
Full
Paper
J. Clin. Invest.,
118(7), 2448-2458, 2008.
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Paper
J. Mol. Biol., 379(1), 28-37, 2008.
Abstract
Full
Paper
J. Biol. Chem., 283(17), 11763-11771, 2008.
Abstract
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Paper
J. Struct. Biol.,
161(1), 18-30, 2008.
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Paper
Protein Pept. Lett.,
14(9), 903-916, 2007.
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Paper
Bioinformatics, 23(24),
3397-3399, 2007.
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Paper
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Abstract
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Proteins, 68(1), 313-323, 2007.
Abstract
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Paper
Proteins, 67(3), 593-605, 2007.
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Full
Paper
Immunol. Allergy Clin. North Am.,
27(1):1-27 2007.
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© 2006 ASM Press, Washington D.C. 257-283.
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2006.
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Peptides, 27(7):1676-1684
2006.
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J. Biol. Chem. 281(12):8051-8061, 2006.
Abstract
Full
Paper
Mol. Immunol.
43(6):509-518, 2006.
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Paper
J. Agric. Food Chem. 53(22):8752-8759, 2005.
Abstract
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Paper
Virol. J. 2(1):40, 2005.
Abstract
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Paper
J. Virol.
79(9):5857-5862, 2005.
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2005.
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Proteins 58(1):200-210,
2005.
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Proc. Natl. Acad. Sci. USA
101(18):6929-6933, 2004.
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11:583-593, 2004.
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Biochemistry 43(3):684-689, 2004.
Abstract
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Paper
J. Virol.
78(1):302-313, 2004.
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Mol. Immunol.
40(8):555-562, 2003.
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Magn. Res.
Chem. 41(S1):S51-S55, 2003.
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J. Agr. Food Chem.
51(16):4830-4837, 2003.
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Biochemistry 42(33):9970-9979,
2003.
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Paper
J. Mol. Model. 9(5):298-303, 2003.
Abstract
Full
Paper
Ivanciuc, O., Schein, C.H. and Braun, W.
SDAP: database and computational tools for
allergenic proteins.
Nucleic Acids Res. 31(1):359-362, 2003.
Abstract
Full
Paper
Mathura, M.S., Schein, C.H. and Braun, W.
Identifying property based sequence motifs in protein
families and superfamilies:
application to DNase-1 related endonucleases.
Bioinformatics 19(11):1381-1390,
2003.
Abstract
Full
Paper
BMC Bioinformatics 3(1):37,
2002.
Abstract
Full
Paper
Bioinformatics 18(10):1358-1364,
2002.
Abstract
Full
Paper
Murtazina, D., Puchkaev, A.V., Schein, C.H., Oezguen, N., Braun, W., Nanavati, A. and Pikuleva, I.A.
Membrane-protein interactions contribute to efficient
27-hydroxylation of cholesterol by mitochondrial
cytochrome P450 27A1.
J. Biol. Chem. 277(40):37582-37589, 2002.
Abstract
Full
Paper
Infect. Immun. 70(8):4485-4493, 2002.
Abstract
Full
Paper
J. Biomol. NMR 22(3):249-263, 2002.
Abstract
Full
Paper
J. Mol. Model. 7(12):445-453, 2001.
Abstract
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Paper
Cell. Biochem. Biophys. 34(3):283-304, 2001.
Abstract
Full Paper Not Available © Humana
Press, INC.
Biophys. J. 81(1):463-472,
2001.
Abstract
Full
Paper
Pac. Symp. Biocomput. 89-100,
2001.
Abstract
Full
Paper
Methods Mol. Biol.
160:263-286, 2001.
Abstract
Full Paper Not Available Online
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148(1):35-46, 2001.
Abstract
Full
Paper
Abstract
Full
Paper
Biophys. J. 79(3):1601-1609,
2000.
Abstract
Full
Paper
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