Complete publication list
131 publications spanning 1977�present, listed in reverse chronological order by publication number.
(131)
Complement Protective Epitopes and CD55-Microtubule Complexes Facilitate the Invasion and Intracellular Persistence of Uropathogenic Escherichia coli
Rana T., Hasan R.J., Nowicki S., Venkatarajan M.S., Singh R., Urvil P.T., Popov V., Braun W., Popik W., Goodwin J.S., Nowicki B.J. � J. Infec. Dis. (2013)
(130)
Assessment of 3D models for allergen research
Power T.D., Ivanciuc O., Schein C.H., Braun W. � PROTEINS: Struct. Funct. and Bioinf. 81(4), 545�554 (2013)
(129)
Membrane fusion triggering: three modules with different structure and function in the upper half of the measles virus attachment protein stalk
Navaratnarajah C.K., Negi S.S., Braun W., Cattaneo R. � J. Biol. Chem. 287(46), 38543�38551 (2012)
(128)
Base of the measles virus fusion trimer head receives the signal that triggers membrane fusion
Apte-Sengupta S., Negi S.S., Leonard V.H.J., Oezguen N., Navaratnarajah C.K., Braun W., Cattaneo R. � J. Biol. Chem. 287(39), 33026�33035 (2012)
(127)
Clostridial toxins: Sensing a target in a hostile gut environment
Oezguen N., Power T.D., Urvil P., Feng H., Pothoulakis C., Stamler J.S., Braun W., Savidge T.C. � Gut Microbes 3(1), 35�41 (2012)
(126)
Engineering proteins with enhanced mechanical stability by force-specific sequence motifs
Lu W., Negi S.S., Oberhauser A.F., Braun W. � Proteins 80(5), 1308�1315 (2012)
(125)
Validation of a Phage Display and Computational Algorithm by Mapping a Conformational Epitope of Bla g 2
Tiwari R., Negi S.S., Braun B., Braun W., Pomes A., Chapman M.D., Goldblum R.M., Midoro-Horiuti T. � Int. Arch. Allergy Immunol. 157(4), 323�330 (2012)
(124)
MD simulation and experimental evidence for Mg2+ binding at the b site in human AP endonuclease 1
Oezguen N., Mantha A.K., Izumi T., Schein C.H., Mitra S., Braun W. � Bioinformation 7(4), 184�198 (2011)
(123)
Host S-nitrosylation inhibits clostridial small molecule-activated glucosylating toxins
Savidge T.C., Urvil P., Oezguen N., et al., Braun W., Stamler J.S., Pothoulakis C. � Nat. Med. 17(9), 1136�1142 (2011)
(122)
AllerML: Markup Language for Allergens
Ivanciuc O., Gendel S.M., Power T.D., Schein C.H., Braun W. � Regul. Toxicol. Pharmacol. 60(1), 151�160 (2011)
(121)
The heads of the measles virus attachment protein move to transmit the fusion-triggering signal
Navaratnarajah C.K., Oezguen N., Rupp L., Kay L., Leonard V.H.J., Braun W., Cattaneo R. � Nat. Struct. Mol. Biol. 18(2), 128�134 (2011)
(120)
An allergen portrait gallery: representative structures and an overview of IgE binding surfaces
Schein C.H., Ivanciuc O., Midoro-Horiuti T., Goldblum R.M., Braun W. � Bioinform. Biol. Insights 4, 113�125 (2010)
(119)
NMR solution structure of poliovirus uridylyated peptide linked to the genome (VPgpU)
Schein C.H., Oezguen N., van der Heden van Noort G.J., Filippov D.V., Paul A., Kumar E., Braun W. � Peptides 31(8), 1441�1448 (2010)
(118)
Automated Detection of Conformational Epitopes using Phage Display Peptide Sequences
Negi S.S., Braun W. � Bioinform. Biol. Insights 3, 71�81 (2009)
(117)
Structural analysis of linear and conformational epitopes of allergens
Ivanciuc O., Schein C.H., Garcia T.I., Oezguen N., Negi S.S., Braun W. � Regul. Toxicol. Pharmacol. 54(3 Suppl), S11�S19 (2009)
(116)
Mechanical stability and differentially conserved physical-chemical properties of Titin Ig-domains
Garcia T.I., Oberhauser A.F., Braun W. � PROTEINS: Struct. Funct. and Bioinf. 75(3), 706�718 (2009)
(115)
The property index PD predicts peptides that cross-react with IgE antibodies
Ivanciuc O., Midoro-Horiuti T., Schein C.H., Xie L., Hillman G.R., Goldblum R.M., Braun W. � Mol. Immunol. 46(5), 873�883 (2009)
(114)
Characteristic Motifs for Families of Allergenic Proteins
Ivanciuc O., Garcia T.I., Torres M., Schein C.H., Braun W. � Mol. Immunol. 46(4), 559�568 (2009)
(113)
Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE
Oezguen N., Zhou B., Negi S.S., Ivanciuc O., Schein C.H., Labesse G., Braun W. � Mol. Immunol. 45(14), 3740�3747 (2008)
(112)
Identification and analysis of conserved motifs in cytochrome P450 family 2
Oezguen N., Kumar S., Hindupur A., Braun W., Muralidhara B.K., Halpert J.R. � J. Biol. Chem. 283(31), 21808�21816 (2008)
(111)
Measles virus blind to its epithelial cell receptor remains virulent in rhesus monkeys
Leonard V.H.J., Sinn P.L., Hodge G., et al., Oezguen N., Braun W., Cattaneo R. � J. Clin. Invest. 118(7), 2448�2458 (2008)
(110)
Unusual Role of a Cysteine Residue in Substrate Binding and Activity of Human AP-Endonuclease 1
Mantha A.K., Oezguen N., Bhakat K.K., Izumi T., Braun W., Mitra S. � J. Mol. Biol. 379(1), 28�37 (2008)
(109)
Dynamic interaction of the measles virus hemagglutinin with its receptor SLAM
Navaratnarajah C.K., Vongpunsawad S., Oezguen N., Stehle T., Braun W., et al. � J. Biol. Chem. 283(17), 11763�11771 (2008)
(108)
Co-Localization of Glyceraldehyde-3-Phosphate Dehydrogenase with Ferredoxin-NADP Reductase in Pea Leaf Chloroplasts
Negi S.S., Carol A., Pandya S., Braun W., Anderson L. � J. Struct. Biol. 161(1), 18�30 (2008)
(107)
Robust quantitative modeling of peptide binding affinities for MHC molecules
Ivanciuc O., Braun W. � Protein Pept. Lett. 14(9), 903�916 (2007)
(106)
InterProSurf: a web server for predicting interacting sites on protein surfaces
Negi S.S., Schein C.H., Oezguen N., Power T.D., Braun W. � Bioinformatics 23(24), 3397�3399 (2007)
(105)
Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces
Negi S.S., Braun W. � J. Mol. Model. 13(11), 1157�1167 (2007)
(104)
A moving metal mechanism for substrate cleavage by DNA repair endonuclease APE-1
Oezguen N., Schein C.H., Peddi S.R., Power T.D., Izumi T., Braun W. � Proteins 68(1), 313�323 (2007)
(103)
Bioinformatics Approaches to Classifying Allergens and Predicting Cross-reactivity
Schein C.H., Ivanciuc O., Braun W. � Immunol. Allergy Clin. North Am. 27(1), 1�27 (2007)
(102)
Structural Database of Allergenic Proteins (SDAP)
Schein C.H., Ivanciuc O., Braun W. � Food Allergy, ASM Press (2006)
(101)
Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus
Negi S.S., Kolokoltsov A.A., Schein C.H., Davey R.A., Braun W. � J. Mol. Model. 12(6), 921�929 (2006)
(100)
NMR structure of the viral peptide linked to the genome (VPg) of poliovirus
Schein C.H., Oezguen N., Volk D.E., Garimella R., Paul A., Braun W. � Peptides 27(7), 1676�1684 (2006)
(99)
Conformational flexibility of mammalian cytochrome P450 2B4 in binding imidazole inhibitors
Muralidhara B.K., Negi S.S., Chin C.C., Braun W., Halpert J.R. � J. Biol. Chem. 281(12), 8051�8061 (2006)
(98)
Structural basis for epitope sharing between group 1 allergens of cedar pollen
Midoro-Horiuti T., Schein C.H., Mathura V., Braun W., et al. � Mol. Immunol. 43(6), 509�518 (2006)
(97)
Common physical-chemical properties correlate with similar structure of the IgE epitopes of peanut allergens
Schein C.H., Ivanciuc O., Braun W. � J. Agric. Food Chem. 53(22), 8752�8759 (2005)
(96)
Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses
Schein C.H., Zhou B., Braun W. � Virol. J. 2(1):40 (2005)
(95)
Nearby clusters of hemagglutinin residues sustain SLAM-dependent canine distemper virus entry
von Messling V., Oezguen N., Zheng Q., Vongpunsawad S., Braun W., Cattaneo R. � J. Virol. 79, 5857�5862 (2005)
(94)
Molluscan attractins, a family of water-borne protein pheromones with interspecific attractiveness
Cummins S.F., Schein C.H., Xu Y., Braun W., Nagle G.T. � Peptides 26, 121�129 (2005)
(93)
Molego-based definition of the architecture and specificity of metal binding sites
Schein C.H., Zhou B., Oezguen N., Mathura V.S., Braun W. � Proteins 58, 200�210 (2005)
(92)
Structural and functional analysis of Aplysia attractins
Painter S.D., Cummins S.F., Nichols A.E., et al., Schein C.H., Braun W., Nagle G.T. � Proc. Natl. Acad. Sci. USA 101, 6929�6933 (2004)
(91)
Using property based sequence motifs and 3D modeling to determine structure and functional regions of proteins
Ivanciuc O., Oezguen N., Mathura V.S., Schein C.H., Xu Y., Braun W. � Curr. Med. Chem. 11, 583�593 (2004)
(90)
Effects of backbone contacts 3' to the abasic site on the cleavage by human AP endonuclease (APE1)
Izumi T., Schein C.H., Oezguen N., Feng Y., Braun W. � Biochemistry 43, 684�689 (2004)
(89)
Selectively receptor-blind measles viruses: identification of residues necessary for SLAM- or CD46-induced fusion
Vongpunsawad S., Oezgun N., Braun W., Cattaneo R. � J. Virol. 78, 302�313 (2004)
(88)
Developing computational tools for NMR: the early days of protein NMR
Braun W. � Magn. Reson. Chem. 41, S51�S55 (2003)
(87)
Major linear IgE epitopes of mountain cedar pollen allergen Jun a 1 map to the pectate lyase catalytic site
Midoro-Horiuti T., Mathura V., Schein C.H., Braun W., et al. � Mol. Immunol. 40, 555�562 (2003)
(86)
A multimeric model for murine anti-apoptotic protein Bcl-2
Mathura V.S., Soman K.V., Varma T.K., Braun W. � J. Mol. Model. 9, 298�303 (2003)
(85)
Detecting potential IgE-reactive sites on food proteins using a sequence and structure database, SDAP-Food
Ivanciuc O., Mathura V., Midoro-Horiuti T., Braun W., Goldblum R., Schein C.H. � J. Agr. Food Chem. 51, 4830�4837 (2003)
(84)
NMR solution structure of attractin, a water-borne protein pheromone from the mollusk Aplysia californica
Garimella R., Xu Y., Schein C.H., Rajarathnam K., Painter S.D., Nagle G.T., Braun W. � Biochemistry 42, 9970�9979 (2003)
(83)
Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases
Mathura V.S., Schein C.H., Braun W. � Bioinformatics 19, 1381�1390 (2003)
(82)
SDAP: database and computational tools for allergenic proteins
Ivanciuc O., Schein C.H., Braun W. � Nucleic Acids Res. 31, 359�362 (2003)
(81)
Total sequence decomposition distinguishes functional modules, molegos in apurinic/apyrimidinic endonucleases
Schein C.H., Ozgun N., Izumi T., Braun W. � BMC Bioinformatics 3:37 (2002)
(80)
Data mining of sequences and 3D structures of allergenic proteins
Ivanciuc O.I., Schein C.H., Braun W. � Bioinformatics 18, 1358�1364 (2002)
(79)
Membrane-protein interactions contribute to efficient 27-hydroxylation of cholesterol by mitochondrial cytochrome P450 27A1
Murtazina D., Puchkaev A.V., Schein C.H., Oezguen N., Braun W., et al. � J. Biol. Chem. 277, 37582�37589 (2002)
(78)
Structure-function analysis of decay-accelerating factor
Hasan R.J., Pawelczyk E., Urvil P.T., et al., Braun W., Nowicki B.J. � Infect. Immun. 70, 4485�4493 (2002)
(77)
Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra
Oezguen N., Adamian L., Xu Y., Rajarathnam K., Braun W. � J. Biomol. NMR 22, 249�263 (2002)
(76)
New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties
Venkatarajan M.S., Braun W. � J. Mol. Model. 7, 445�453 (2001)
(75)
Homology modeling and simulations of nuclease structures
Soman K.V., Schein C.H., Zhu H., Braun W. � Methods Mol. Biol. 160, 263�286 (2001)
(74)
The protein non-folding problem: amino acid determinants of intrinsic order and disorder
Williams R.M., Obradovic Z., Mathura V., Braun W., et al. � Pac. Symp. Biocomput. 89�100 (2001)
(73)
Determining the 3-D fold of a protein from approximate constraints: a simulation study
Soman K.V., Braun W. � Cell Biochem. Biophys. 34, 283�304 (2001)
(72)
Aplysia attractin: biophysical characterization and modeling of a water-borne pheromone
Schein C.H., Nagle G.T., Page J., Sweedler J.V., Xu Y., Painter S.D., Braun W. � Biophys. J. 81, 463�472 (2001)
(71)
Automatic assignment of NOESY cross peaks and determination of the protein structure of a New World scorpion neurotoxin
Xu Y., Jablonsky M.J., Jackson P.L., Braun W., Krishna N.R. � J. Magn. Reson 148, 35�46 (2001)
(68)
MASIA: recognition of common patterns and properties in multiple aligned protein sequences
Zhu H., Schein C., Braun W. � Bioinformatics 16, 950�951 (2000)
(67)
Homology modeling and characterization of IgE binding epitopes of mountain cedar allergen Jun a 3
Soman K.V., Midoro-Horiuti T., Ferreon J.C., Goldblum R.M., Brooks E.G., Kurosky A., Braun W., Schein C.H. � Biophys. J. 79, 1601�1609 (2000)
(66)
Homology modeling and molecular dynamics simulations of PBCV-1 glycosylase complexed with UV-damaged DNA
Zhu H., Schein C.H., Braun W. � J. Mol. Model. 5, 302�316 (1999)
(65)
Automated 2D NOESY assignment and structure calculation of crambin(S22/I25) with NOAH/DIAMOD
Xu Y., Wu J., Gorenstein D., Braun W. � J. Magn. Reson. 136, 76�85 (1999)
(63)
Sequence specificity, statistical potentials and 3D structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins
Zhu H., Braun W. � Protein Science 8, 326�342 (1999)
(62)
Allostery in rabbit pyruvate kinase: development of a strategy to elucidate the mechanism
Friesen R.H.E., Castellani R.J., Lee J.C., Braun W. � Biochemistry 37, 15266�15276 (1998)
(61)
Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules
Fraczkiewicz R., Braun W. � J. Comp. Chem. 19, 319�333 (1998)
(60)
Mapping of the primary binding site of measles virus to its receptor CD46
Buchholz C.J., Koller D., Devaux P., Mumenthaler Ch., Schneider-Schaulis J., Braun W., Gerlier D., Cattaneo R. � J. Biol. Chem. 272, 22072�22079 (1997)
(59)
Automated combined assignment of NOESY spectra and three-dimensional protein structure determination
Mumenthaler Ch., G�ntert P., Braun W., W�thrich K. � J. Biomol. NMR 10, 351�362 (1997)
(58)
A 3D model for the measles virus receptor CD46 based on homology modeling, Monte Carlo simulations and hemagglutinin binding studies
Mumenthaler Ch., Schneider U., Buchholz C.J., Koller D., Braun W., Cattaneo R. � Protein Sci. 6, 588�597 (1997)
(56)
Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry
Mumenthaler Ch., Braun W. � J. Mol. Biol. 254, 465�480 (1995)
(55)
Folding of globular proteins by energy minimization and Monte Carlo simulations with hydrophobic surface area potentials
Mumenthaler Ch., Braun W. � J. Mol. Modeling 1, 1�10 (1995)
(54)
Predicting the helix packing of globular proteins by self-correcting distance geometry
Mumenthaler Ch., Braun W. � Protein Science 4, 863�871 (1995)
(53)
Three dimensional structure and action of immunosuppressants and their immunophilins
Braun W., Kallen J., Mikol V., Walkinshaw M.D., W�thrich K. � FASEB Journal 9, 63�72 (1995)
(51)
Conformational polymorphism of cyclosporin A
Altschuh D., Braun W., Kallen J., Mikol V., et al., W�thrich K. � Structure 2, 963�972 (1994)
(50)
Determination of the NMR solution structure of the Cyclophilin-Cyclosporin A complex
Spitzfaden C., Braun W., Wider G., Widmer H., W�thrich K. � J. Biomol. NMR 4, 463�482 (1994)
(49)
Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin
H�nggi G., Braun W. � FEBS Letters 344, 147�153 (1994)
(48)
Surface area included in energy refinement of proteins: A comparative study on atomic solvation parameters
von Freyberg B., Richmond T.J., Braun W. � J. Mol. Biol. 233, 275�292 (1993)
(47)
Extensive distance geometry calculations with different NOE calibrations
Widmer H., Widmer A., Braun W. � J. Biomol. NMR 3, 307�324 (1993)
(46)
Minimization of empirical energy functions in proteins including hydrophobic surface area effects
von Freyberg B., Braun W. � J. Comp. Chem. 14, 510�521 (1993)
(45)
Comparison of the NMR solution structure and the X-ray crystal structure of rat metallothionein-2
Braun W., Vasak M., Robbins A.H., Stout C.D., Wagner G., K�gi J.H.R., W�thrich K. � Proc. Natl. Acad. Sci. USA 89, 10124�10128 (1992)
(44)
Cyclosporin A - cyclophilin complex: a model based on X-ray and NMR data
Spitzfaden C., Weber H.P., Braun W., Kallen J., et al., W�thrich K. � FEBS Letters 300, 291�300 (1992)
(43)
Receptor-Induced Conformation Change of the Immuno-suppressant Cyclosporin-A
W�thrich K., von Freyberg B., Weber C., et al., Braun W. � Science 254(5034), 953�954 (1991)
(42)
Complete relaxation matrix refinement of NMR structures of proteins
Mertz J.E., G�ntert P., W�thrich K., Braun W. � J. Biomol. NMR 1, 257�269 (1991)
(40)
The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution
Weber Ch., Wider G., von Freyberg B., Traber R., Braun W., et al., W�thrich K. � Biochemistry 30, 6563�6574 (1991)
(39)
Efficient search for all low energy conformations of polypeptides by Monte Carlo methods
von Freyberg B., Braun W. � J. Comp. Chem. 12, 1065�1076 (1991)
(37)
Two-dimensional 1H NMR study of AaH IT, an anti-insect toxin from the scorpion Androctonus australis Hector
Darbon H., Weber Ch., Braun W. � Biochemistry 30, 1836�1845 (1991)
(36)
Efficient computation of three dimensional protein structures in solution from NMR data using DIANA
G�ntert P., Braun W., W�thrich K. � J. Mol. Biol. 217, 517�530 (1991)
(33)
A program, FANTOM, for energy refinement of Polypeptides and Proteins
Schaumann Th., Braun W., W�thrich K. � Biopolymers 29, 679�694 (1990)
(30)
Comparison of the high-resolution structures of the a-amylase inhibitor Tendamistat determined by NMR and X-ray
Billeter M., Kline A.D., Braun W., Huber R., W�thrich K. � J. Mol. Biol. 206, 677�687 (1989)
(29)
Solution of the Phase Problem in the X-ray Diffraction Method with the NMR structure as initial model
Braun W., Epp O., W�thrich K., Huber R. � J. Mol. Biol. 206, 669�676 (1989)
(28)
Automated stereospecific 1H-NMR assignments and their impact on the precision of protein structure determination
G�ntert P., Braun W., Billeter M., W�thrich K. � J. Amer. Chem. Soc. 111, 3997�4004 (1989)
(27)
Determination of the Complete Three-Dimensional Structure of the a-Amylase Inhibitor Tendamistat
Kline A.D., Braun W., W�thrich K. � J. Mol. Biol. 204, 675�724 (1988)
(21)
Distance Geometry and related methods for protein structure determination from NMR data
Braun W. � Quart. Rev. Biophysics 19, 115�157 (1987)
(20)
Protein structures in solution by NMR and distance geometry
Wagner G., Braun W., Havel T.F., Schaumann T., Go N., W�thrich K. � J. Mol. Biol. 196, 611�641 (1987)
(13)
Calculation of protein conformations by proton-proton distance constraints: A new efficient algorithm
Braun W., Go N. � J. Mol. Biol. 186, 611�626 (1985)
(12)
Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances
W�thrich K., Billeter M., Braun W. � J. Mol. Biol. 180, 715�740 (1984)
(3)
Combined use of proton-proton Overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations
Braun W., B�sch C., Brown L.R., Go N., W�thrich K. � Biochim. Biophys. Acta 667, 377�396 (1981)
(1)
The Vlasov dynamics and its fluctuations in the 1/N limit of interacting classical particles
Braun W., Hepp K. � Commun. Math. Phys. 56, 101�113 (1977)