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Tenure-Track Faculty
Robert J Woods
Professor of Biochemistry and Molecular Biology, and Chemistry

The relationships between the conformations of carbohydrate molecules and biological recognition and activity

Telephone: 706-542-4454
Fax: 706-542-4412

Short Biography
Research Interests
Lab-personal web site

Short Biography:
Dr. Woods received both his B.Sc.(Honors) in engineering chemistry in 1985 and his Ph.D. in 1990 in computational and synthetic organic chemistry from Queen's University in Kingston, Ontario, Canada. He joined the CCRC in January 1995. Dr. Woods is a senior investigator on a technological research and development project of the National Institutes of Health Resource Center for Biomedical Complex Carbohydrates. He has been invited to write an entry on carbohydrate force fields for the Encyclopedia of Computational Chemistry. He is a member of UGA's Campus Information Technology Forum and the UGA Modeling Laboratory Operations Committee, and has made recent presentations at the International Carbohydrate Symposium, the Gordon Research Conferences, and the National Research Council of Canada. Full publications: 33.

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Research Interests:
Dr. Woods's research examines the relationships between the conformations of carbohydrate molecules and biological recognition and activity, particularly the mechanisms involved in carbohydrate recognition in immunological events. Significant alterations in the biological activities of peptides and proteins often accompany the covalent attachment of an oligosaccharide (glycosylation) to one or more of their amino acid residues. Approximately 60% of all mammalian proteins are glycosylated, and the glycoproteins that are generated by glycosylation are also frequently found attached to the cell surfaces of bacteria, fungi, and parasites.

But the roles of oligosaccharide moieties are extremely diverse. In mucins, for example, the carbohydrate component of a glycoprotein may be present in a largely structural capacity, whereas in human chorionic gonadotropin or tissue plasminogen activator it alters the functioning of the protein. The carbohydrate component may also be the part of the glycoprotein recognized by the immune system, directly affecting antibody-antigen interactions, self- and non-self-recognition, and auto-immune disorders. Recognition by the host�s immune system of the carbohydrate portion of the glycoproteins of these pathogenic microorganisms is essential for an immune response to be generated by the host. Moreover, an understanding of the factors that enable antibodies to distinguish among glycoproteins is essential to the rational development of vaccines. Elucidating the conformational properties of glycoproteins and their carbohydrate components is key to this understanding. Dr. Woods�s investigations seek to define the conformational properties of the free oligosaccharides of such glycoproteins, the effect of attachment of the oligosaccharide to the protein, and the mechanisms of non-covalent oligosaccharide-protein interactions.

Traditional experimental techniques that have been successfully applied to proteins have not been able to determine conclusively the conformational properties of glycoproteins. The conformation of an oligosaccharide in aqueous solution is determined by interactions (both steric and electronic and between both attached and nonbonded atoms) between the sugar residues and between these residues and solvent molecules. All these interatomic interactions must be adequately described in order to arrive at an accurate prediction of an oligosaccharide's conformational preferences. Moreover, the structure may need to be described as an ensemble of conformations rather than as a single conformation, accounting for both spatial and temporal properties of the oligosaccharide. Mathematically, such a description can be obtained by applying a molecular mechanical force field in molecular dynamics (MD) simulations, a standard technique in the analysis of protein and oligonucleotide structures.

Dr. Woods's group utilizes, in conjunction with experimental methods (e.g., 2D 1H-NMR spectroscopy), the computational techniques of molecular dynamics (MD) and free energy perturbation simulations to elucidate the conformational properties of oligosaccharides. Simulations are in no way constrained to reproduce the experimental data. The computational simulations use the all-atom AMBER force field for proteins and nucleic acids and a novel set of parameters developed by Dr. Woods's group for use with carbohydrates, GLYCAM. The GLYCAM parameters make it possible to probe the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics and compare these directly with experimental NMR data that are often consistent with numerous possible conformations. These parameters are currently suitable for all biologically relevant N- and O-linkages in oligo- and polysaccharides and glycoproteins.

Current research projects using these techniques include examinations of bacterial antigen-antibody interactions, as well as carbohydrate-lectin interactions. Carbohydrate antigens associated with Salmonella paratyphi B and group B Streptococcus are being studied to understand the energetic contributions hydrophobic and hydrophilic interactions make to antibody binding energy. More applied aspects of the research include the screening of synthetic combinatorial peptide libraries for peptides that bind to carbohydrate receptor proteins (antibodies and lectins) and their subsequent co-crystallization with the receptor. Peptides are characteristically more antigenic than carbohydrates, and the Woods laboratory�s interest in carbohydrate mimics is driven by a desire to produce non-carbohydrate molecules that can either act as anti-bacterial vaccines or inhibit auto-immune reactions.

Dr. Woods's research is supported by the National Institutes of Health and the National Science Foundation.

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Publications: Author's Last Name: Woods

Journal Articles
Book Chapters are listed at the bottom of this page.

T Turney, Q Pan, L Sernau, I Carmichael, W Zhang, X Wang, RJ Woods, AS Serianni. 20156. O-Acetyl Side-Chains in Monosaccharides: Redundant NMR Spin-Couplings and Statistical Models for Acetate Ester Conformational Analysis. J Phys Chem B 121(1): 66-77. PMID:28001427

N Nemanachvili, I Tomris, HL Turner, R McBride, OC Grant, R van der Woude, MH Aldosari, RJ Pieters, RJ Woods, JC Paulson, GJ Boons, AB Ward, MH Verheije, RP de Vries. 2019. Fluorescent trimeric hemagglutinins reveal multivalent receptor binding properties. J Mol Biol 431(4): 842-856.

S Neelamegham, K Aoki-Kinoshita, E Bolton, M Frank, F Lisacek, T Lutteke, N O'Boyle, NH Packer, P Stanley, P Toukach, A Varki, RJ Woods, A Darvill, A Dell, B Henrissat, C Bertozzi, G Hart, H Narimatsu, H Freeze, I Yamada, J Paulson, J Prestegard, J Marth, JFG Vliegenthart, M Etzler, M Aebi, M Kanehisa, N Taniguchi, N Edwards, P Rudd, P Seeberger, R Mazumder, R Ranzinger, R Cummings, R Schnaar, S Perez, S Kornfeld, T Kinoshita, W York, Y Knirel, SD Grp. 2019. Updates to the Symbol Nomenclature for Glycans guidelines. Glycobiology Aug 20; 29(9): 620-624. PMID:31184695

GR Chalmers, A Eletsky, LC Morris, JY Yang, F Tian, RJ Woods, KW Moremen, JH Prestegard. 2019. NMR Resonance Assignment Methodology: Characterizing Large Sparsely Labeled Glycoproteins,. J Molecular Biology 431: 2369-2382. PMID:31034888

Y Zhao, JY Yang, DF Thieker, Y. Xu, C. Zong, G-J Boons, Z.-J. Liu, RJ Woods, KW Moremen, IJ Amster. 2018. A traveling wave ion mobility spectrometry (TWIMS) study of the Robo 1-heparan sulfate interaction. J Am Soc Mass Spectrom 29(6): 1153-1165. PMID:29520710

D Thieker, Y Xu, D Chapla, C Nora, H Qiu, T Felix, L Wang, KW Moremen, J Liu, J Esko, RJ Woods. 2018. Downstream products are potent inhibitors of the heparan sulfate 2-O-sulfotransferase . Scientific Reports 8: 11823-. PMID:30087361

Y. Zhao, A. Singh, Y. Xu, C. Zong, F. Zhang, G.J. Boons, J. Liu, R.J. Linhardt, R.J. Woods, I.J. Amster. 2017. Gas-phase analysis of the complex of fibroblast growth factor 1 with heparan sulfate: A traveling wave ion mobility spectrometry (TWIMS) and molecular modeling study. J. Am. Soc. Mass Spectrom. 28(1): 96-109. PMID:27663556

X Li, OC Grant, K Ito, A Wallace, S Wang, P Zhao, L Wells, S Lu, RJ Woods, JS Sharp. 2017. Structural Analysis of the Glycosylated Intact HIV-1 gp120-b12 Antibody Complex Using Hydroxyl Radical Protein Footprinting. Biochemistry Feb 21;56(7): 957-970. PMID:28102671

A Sood, OO Gerlitis, Y Ji, NV Bovin, L Coates, RJ Woods. 2017. Approaching the Problem of Carbohydrates Specificity from a Pharmacophore Perspective. J Biol Chem Submitted: -.

W Peng, K Bouwman, R McBride, OC Grant, RJ Woods, M Veheije, J Paulson , R de Vries. 2017. Enhanced human-type receptor binding by ferret transmissible H5N1 with a K193T mutation. J Virology Submitted: -.

MK Misra, A Sood, PA Soares, VH Pomin, RJ Woods, JS Sharp. 2017. Mapping of the Fondaparinux Binding Site of JR-FL gp120 by High Resolution Hydroxyl Radical Protein Footprinting and Computational Docking. PLoS One Submitted: -.

M.O. Sheikh, D.F. Thieker, G. Chalmers, C.M. Schafter, M. Ishihara, P. Azadi, R.J. Woods, J.N. Glushka, B. Bendiak, J.H. Prestegard, C.M. West. 2017. 02 Sensing associated glycosylation exposes the F-box combining site of the Dictyostelium Skp1 subunit in E3 ubiquitin ligases. J. Biol. Chem. 46: 18897-18915. PMID:28928219

OO Gerlits, L Coates, RJ Woods, A Kovalevsky. 2017. Mannobiose Binding Induces Changes in Hydrogen Bonding and Protonation States of Acidic Residues in Concanavalin A as Revealed by Neutron Crystallography . Biochemistry 56(36): 4747-4750. PMID:28846383

Y Ji, YJ White, JA Hadden, OC Grant, RJ Woods. 2017. New Insights into Influenza A Specificity: An Evolution of Paradigms. Curr Opin Struct Biol 44: 219-231. PMID:28675835

BM Xie, A Sood, RJ Woods, JS Sharp. 2017. Quantitative Protein Topography Measurements by High Resolution Hydroxyl Radical Protein Footprinting Enable Accurate Molecular Model Selection. Sci Rep 7: 4552-. PMID:28674401

RP de Vries, W Peng, O Grant, A Thompson, X Zhu, K Bouwman, A Torrents de la Pena, M van Breemen, I Ambepitiya, C de Haan, W Yu, R McBride, R Sanders, RJ Woods, M Verheije, I Wilson, J Paulson. 2017. Three mutations switch H7N9 influenza to human-type receptor specificity. PLoS Pathogens 13(6): e1006390-. PMID:28617868

W Zhang, T Turney, R Meredith, Q Pan, L Sernau, X Wang, X Hu, RJ Woods, I Carmichael, A Serianni. 2017. Conformational Populations of beta-(1-4)O-Glycosidic Linkages Using Redundant NMR J-Couplings and Circular Statistics. J Phys Chem B 121(14): 3042-3058. PMID:28296420

Z Wang, P-H Hsieh, Y Xu, D Thieker, E Chai, S Xie, B Cooley, RJ Woods, L Chi, J Liu. 2017. Synthesis of 3-O-Sulfated Oligosaccharides to Understand the Relationship between Structures and Functions of Heparan Sulfate. J Am Chem Soc 139(14): 5249-5256. PMID:28340300

J Yu, OC Grant, C Pett, S Strahl, RJ Woods, U Westerlind. 2017. Induction of Antibodies Directed Against Branched Core O-Mannosyl Glycopeptides - Selectivity Complimentary to the ConA Lectin. Chemistry 23(14): 3466-3473. PMID:28079948

W Peng, RP de Vries, OC Grant, AJ Thompson, R MBridge, B Tsogtbaatar, PS Lee, N Razi, IA Wilson, RJ Woods, JC Paulson. 2017. Recent H3N2 Viruses Have Evolved Specificity for Extended, Branched Human-type Receptors, Conferring Potential for Increased Avidity. Cell Host Microbe 21(1): 23-24. PMID:28017661

J Hopper, A Ambrose, OC Grant, S Krumm, T Allison, MT Degiacomi, M Tully, L Pritchard, G Ozorowski, A Ward, M Crispin, K Doores, RJ Woods, J Benesch, CV Robinson, WB Struwe. 2017. The Tetrameric Plant Lectin BanLee Neutralizes HIV through Bidentate Binding to Specific Viral Glycans. Structure 25(5): 773-782. PMID:28434916

K Khatri, JA Klein, MR White, OC Grant, N Leymarie, RJ Woods, KL Hartshorn, J Zaia. 2016. Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions. Mol Cell Proteomics 15: 1895-1912. PMID:26984886

C-H Hsu, S Park, D Mortenson, BL Foley, X Wang, RJ Woods, D Case, E Powers, C-H Wong, HJ Dyson, J Kelly. 2016. The Dependence of Carbohydrate Aromatic Interaction Strengths on the Structure of the Carbohydrate. J Am Chem Soc June 14: -. PMID:27249581

X Wang, RJ Woods. 2016. Insights into Furanose Solution Conformations: Beyond the Two-State Model. J Biomol NMr 64: 291-305. PMID:26968894

A Singh, MB Tessier, K Pederson, X. Wang, A. Venot, GJ Boons, JH Prestegard, RJ Woods. 2016. Extension and Validation of the GLYCAM Force Field Parameters for modeling Glycosaminoglycans. Canadian Journal of Chemistry 94(11): 927-935.

G Chalmers, JN Glushka, BL Foley, RJ Woods, JH Prestegard. 2016. Direct NOE simulation from long MD trajectories. Journal of Magnetic Resonance 265: 1-9. PMID:26826977

DF Thieker, JA Hadden, K Schulten, RJ Woods. 2016. 3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans. Glycobiology 26(8): 786-787. PMID:27514939

OC Grant, X Xue, D Rahbarania, A Khatamian, BL Foley, RJ Woods. 2016. Gly-Spec: a web tool for predicting glycan specificity by integrating glycan array screening data and 3D structure. Glycobiology 26(10): 1027-1028. PMID:28120784

P Hsieh, D Thieker, M Guerinni, RJ Woods, J Liu. 2016. Uncovering the Relationship between Sulphation Patterns and Conformation of Iduronic Acid Heparan Sulphate. Sci Rep 6: 29602-. PMID:27412370

Z Sumer-Bayraktar, OC Grant, V Venkatkrishnan, RJ Woods, NH Packer, M Thaysen-Andersen. 2016. Asn347-Glycosylation of Corticosteroid Binding Globulin Fine-Tunes the Host Immune Response by Modulating Proteolysis by P. aeruginosa and Neutrophil Elastase. J Biol Chem 291(34): 17727-17742. PMID:27339896

A Singh, WC Kett, IC Severin, I Agyekum, J Duan, IJ Amster, AEI Proudfoot, DR Coombe, RJ Woods. 2015. The Interaction of Heparin Tetrasaccharides with Chemokine CCL5 is Modulated by Sulfation Pattern and pH. J. Biol. Chem. Apr 23: -. PMID:25907556

I*** Hang, C Lin, OC Grant, S Fleurkens, TK Villiger, M Soos, M Morbidelli, RJ Woods, R Gauss, MP Aebi. 2015. Generating diversity-mechanism of site-specific N-glycan remodeling in the ER and the Golgi. EMBOJ, submitted : -.

VM Krishanmurthy, S Sardar, Y. Yu, X. Song, C Haller, E. Dai, X. Wang, DR Hanjaya-Putra, L. Sun, V Morikis, S Simon, RJ Woods, R Cummings, E Chaikof. 2015. Glycopeptide Analogues of PSGL-1 Inhibit P-Selectin In Vitro and In Vivo. Nature Communications 6: 1-12. PMID:25824568

I Queiroz, X. Wang, J. Glushka, G Santos, A-P Valente, J.H. Prestegard, RJ Woods, P.A. Mourao, V.H. Pomin. 2015. Impact of sulfating pattern on the conformation and dynamics of sulfated fucan oligosaccharides as revealed by NMR and MD. Glycobiology 25: 535-547. PMID:25527427

I Hang, C Lin, OC Grant, S Fleurkens, TK Villiger, M Soos, M Morbidelli, RJ Woods, R Gauss, M Abei. 2015. Analysis of site-specific N-glycan remodeling in the endoplasmic reticulum and the Golgi. Glycobiology 12: 1335-49. PMID:26240167

OC Grant, MB Tessier, L Meche, LK Mahal, BL Foley, RJ Woods. 2015. Combining 3D Structure with Glycan Array Data Provides Insight into the Origin of Glycan Specificity . Glycobiology 26(7): 772-783. PMID:26911287

A Nivedha, D Thieker, S Makeneni, H Hu, RJ Woods. 2015. Vina-Carb: Improving Glycosidic Angles During Carbohydrate Docking. J Chem Theor Comput 12(2): 892-901. PMID:26744922

J.A. Hadden, A.D. French, R.J. Woods. 2014. Effect of microfibril twisting on theoretical powder diffraction patterns of cellulose l beta. Cellulose 21(2): 879-884. PMID:24729665

S Ng, E Lin, PI Kitov, KF Tjhung, OO Gerlits, L Deng, B Kasper, A Sood, BM Paschal, JS Klassen, CJ Noren, LK Mahal, RJ Woods, L Coates, R Derda. 2014. Genetically-Encoded Fragment-based Discovery of Glycoprotein ligands for Carbohydrate binding Proteins. J Am Chem Soc 137(16): 5248-5251. PMID:25860443

C Panagos, D Thomson, C. Moss, AD Hughes, MS Kelly, Y Liu, W Chai, R Venkatasamy, D Spina, CP Page, J Hogwood, RJ Woods, B Mulloy, CD Bavington, D Uhrin. 2014. Fucosylated Chondroitin Sulfates from the Body Wall of the Sea Cucumber Holothuria Forskali. Conformation, Selectin Binding and Biological Activity. J. Biol. Chem. 289(41): 28284-28298. PMID:25147180

S Makeneni, BL Foley, RJ Woods. 2014. BFMP: A Method for Discretizing and Visualizing Pyranose Conformations. J. Chem. Inf. Model 54: 2744-2750. PMID:25289680

P Lak, S Makeneni, RJ Woods, T Lowary. 2014. Specificity of Furanoside-Protein Recognition through Antibody Engineering and Molecular Modeling. Chem. Eur. J. 20: 1-12. PMID:25413161

OC Grant, RJ Woods. 2014. Recent Advances in Employing Molecular Modeling to Determine the Specificity of Glycan-binding Proteins. Curr. Opin. Struct. Biol. 28C: 47-55. PMID:25108191

S Makenemi, Y Ji, DC Watson, NM Young, RJ Woods. 2014. Predicting the origins of anti-blood group antibody specificity: A case study of the ABO A- and B-antigens. Frong. Immunol. - Immunotherapies and Vaccines 5: 397-408. PMID:25202309

TA Poor, LM Jones, A Sood, GP Leser, MD Plasencia, DL Rempel, TS Jardetzky, RJ Woods, ML Gross. 2014. Probing the paramyxovirus fusion (F) protein-refolding event from pre- to post fusion by oxidative footprinting. PNAS 111: E2596-2605. PMID:24927585

M.B. Tessier, O.C. Grant, J. Heimburg-Molinaro, D. Smith, S. Jadey, A.M. Gulick, J. Glushka, S.L. Deutscher , K. Ritenhouse-Olson, R.J. Woods. 2013. Computational screening of the human TF-glycome provides a structural definition for the specificity of anti-tumor antibody JAA-F11. PLoS One 8: e54874-. PMID:23365681

L. Meng, F. Forouhar, D. Thieker, Z. Gao, A. Ramiah, H.A. Moniz, J. Seetharaman, S. Milaninia, M. Su, R. Bridger, L. Veillon, P. Azadi, G. Kornhaber, L. Wells, G.T. Montelione, R.J. Woods, L. Tong, K.W. Moremen. 2013. Enzymatic basis for N-glycan sialylation: Structure of mammalian alpha2,6-sialytransferase (ST6GAL1) reveals conserved and unique features for glycan sialytion. J. Biol. Chem. 288(48): 34680-34698. PMID:24155237

J.A. Hadden, A.D. French, R.J. Woods. 2013. Unraveling cellulose microfibrils: A twisted tale. Biopolymers 99: 746-756. PMID:23681971

A Siriwardena, KK Pulukuri, PS Kandiyal, S Roy, O Bande, S Ghosh, JMG Fernandez, FA Martin, J-M Ghigo, C Beloin, K Ito, RJ Woods, RS Ampapathi, TK Chakraborty. 2013. Sugar-Modified Foldamers as Conformationally Defined and Biologically Distinct Glycopeptide Mimics. Ange Chem 125: 10411-10416. PMID:23943598

NT Wood, E Fadda, R.J. Davis, OC Grant, JC Martin, RJ Woods, SA Travers. 2013. The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop. PLoS One 8: e80301-. PMID:24303005

JC Martin, E Fadda, K Ito, RJ Woods. 2013. Defining the Structural Origin of the Substrate Sequence Independence of O-GlcNAcase Using a Combination of a Molecular Docking and Dynamics Simulation. Glycobiology 24: 85-96. PMID:24134879

OC Grant, HM Smith, D Firsova, E Fadda, RJ Woods. 2013. Presentation, Presentation, Presentation! Molecular Level Insight into Linker Effects on Glycan Array Screening Data. Glycobiology 24: 17-25. PMID:24056723

AK Nivedha, S Makeneni, BL Foley, M Tessier, RJ Woods. 2013. The Importance of Ligand Conformational Energies in Carbohydrate Docking: Sorting the Wheat from the Chaff. J Comput Chem 35: 526-539. PMID:24375430

E Fadda, RJ Woods. 2013. Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase QM calculations. Can J Chem 91: 1-7. PMID:25418993

M.B. Tessier, O,.C. Grant, J. Heimburg-Molinaro, D. Smith, S. Jadey, A.M. Gulick, J. Glushka, S.L. Deutscher, K. Rittenhouse-Olson, R.J. Woods. 2012. Computational screening of the human TF-glycome provides a structural definition for the specificity of anti-tumor antibody JAA-F11. PLoS One 8: -. PMID:23365681

B. Sattelle, B. Bose-Basu, M.B. Tessier, R.J. Woods, A.S. Serianni, A. Almond. 2012. The dependence of pyranose ring puckering on anomeric configuration: Methyl idopyranosides. J. phys. Chem. B 116: 6380-6386. PMID:22577942

M.A. Johnson, J. Cartmell, N.E. Weisser, R.J. Woods, D.R. Bundle. 2012. Molecular recognition of candida albicans (1-->2)-beta-mannan oligosaccharides by a protective monoclonal antibody reveals the immunodominance of internal saccharide residues. J. Biol. Chem. 287: 18078-18090. PMID:422493450

LRI Davies, OMT Pearce, MB Tessier, S Assar, V Smutova, M Pajunen, M Sumida, C Sato, K Kitajima, J Finne, P Gagneux, A Pshezhetsky, RJ Woods, A Varki. 2012. Metabolism of Vertebrate Amino Sugars with N-glycolyl Groups: Resistance of a alpha 2-8-linked N-glycolylneuraminic Acid to Enzymatic Cleavage. J Biol Chem 287: 28917-28931. PMID:22692207

E Ficko-Blean, C Stuart, MB Suits, MB Tessier, RJ Woods, AT Boraston. 2011. Carbohydrate recognition by an architecturally complex alpha-N-Acetylglucosaminidase from Clostridium perfringens. PLoS One 7(3): e33524-. PMID:22479408

BF Foley, M Tessier, RJ Woods. 2011. Carbohyrate Force Fields. WIREs Comput Mol Sci 2: 1-46.

ML DeMarco, RJ Woods. 2011. From agonist to antagonist: structure and dynamics of innate immune glycoprotein MD-2 upon recognition of variably acylated bacterial endotoxins. Mol Immunol 49: 124-133. PMID:21924775

E Fadda, RJ Woods. 2011. On the role of water models in quantifying the standard binding free energy of highly conserved water molecules in proteins: the case of Concanavalin A. J Comput Theor Chem 7: 3391-3398. PMID:26598169

PJ Brett, MN Burtnick, C Heiss, P Azadi, D DeShazer, DE Woods, FC Gherardini. 2011. Burkholderia thailandenis oacA mutants facilitate the expression of Burkholderia mallei-like O polysaccharides. Infect Immun 79(2): 961-969. PMID:21115721

R Kadirvelraj, O Grant, IJ Goldstein, HC Winter, H Tateno, E Fadda, RJ Woods. 2011. Structure and Binding Analysis of Polyporus squamosus Lectin in Complex with the Neu5Ac(alpha)2-6Gal(beta)1-4G1cNAc Human-type Influenza Receptor. Glycobiology 21(7): 973-984. PMID:21436237

R Ju, M Tessier, L Olliff, RJ Woods, A Summers, Y Geng. 2011. Supramolecular Dendrimer Capsules by Cooperative Binding. Chem Commun 47: 268-270. PMID:20689873

E Fadda, RJ Woods. 2010. Molecular Simulations of Carbohydrates and Protein-carbohydrate Interactions: Motivation, Issues and Prospects. Drug Disc Today 15: 596-609. PMID:20594934

RJ Woods, M Tessier. 2010. Computational Glycoscience: Characterizing the Spatial and Temporal Properties of Glycans and Glycan-Protein Complexes. Curr Opin Struct Biol 20: 1-9. PMID:20708922

M.L. DeMarco, R.J. Woods. 2009. Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer, and its implications for ganglioside-protein recognition at membrane surfaces. Glycobiology 19: 344-355. PMID:19056784

C. Watson, I. Janik, T. Zhuang, O. Charvatova, R.J. Woods, J.S. Sharp. 2009. Pulsed electron beam water radiolysis for submicrosecond hydroxyl radical protein footprinting. Anal. Chem. 81: 2496-2505. PMID:19265387

M.L. DeMarco, R.J. Woods, J. Prestegard, F. Tian. 2009. Presentation of membrane-anchored glycosphingolipids determined from molecular dynamics simulations and NMR paramagnetic relaxation rate enhancement. J. Am Chem. Soc. 132: 1344-1388. PMID:20092028

K.N. Kirschner, A.B. Yongye, S.M. Tschampel, J. Gonzalez-Outeirino, C.R. Daniels, B.L. Foley, R.J. Woods. 2008. GLYCAM06: A generalizable biomolecular force field. Carbohydrates. J. Comput. Chem. 29: 622-655. PMID:17849372

M.B. Tessier, M.L. DeMarco, A.B. Yongye, R.J. Woods. 2008. Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids. Mol Simulation 34: 349-364.

M.L. DeMarco, R.J. Woods. 2008. Structural biology: a game of snakes and ladders. Glycobiology 18: 426-440. PMID:18390826

A.B. Yongye, B.L. Foley, R.J. Woods. 2008. On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol. J. Phys. Chem. B. 112: 2634-2639. PMID:18311953

M. Seo , N. Castillo, R. Ganzynkowicz, C.R. Daniels, R.J. Woods, P.-N. Roy, T.L. Lowary. 2008. An approach for the simulation and modeling of flexible rings. Application to the alpha-D-arabinofuranoside ring, a key constitutent of polyscccharides from Mycobaterium tuberculosis. J. Chem Theory Comput. 4: 184-191.

A.B. Yongye, J. Gonzalez-Outerino, J. Glushka, V. Schulteis, R.J. Woods. 2008. The conformational properties of methyl alpha-(2,8)-di/trisialosides and their N-acyl analogues: implications for anti-Neisseria meningitidis B vaccine design. Biochemistry 47: 12493-12514. PMID:18954144

O. Charvatova, B.L. Foley, M. Bern, J. Sharp, R. Orlando, R.J. Woods. 2008. Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1. J. Am. Soc. Mass Spectrom. 19: 1692-1705. PMID:18707901

R. Kadirvelraj, B.L. Foley, J.D. Dyekjaer, R.J. Woods. 2008. Involvement of water in carbohydrate-protein binding: concanavalin A revisited. J. Am. Chem. Soc. 130: 16933-16942. PMID:19053475

N.T. Seyfried, J.A. Atwood,, A. Yongye, A. Almond, A.J. Day, R. Orlando, R.J. Woods. 2007. Fourier transform mass spectrometry to monitor hyaluronan-protein interactions: use of hydrogen/deuterium amide exchange. Rapid Commun. Mass Spectrom. 21: 121-131. PMID:17154353

D. Elking, T. Darden, R.J. Woods. 2007. Gaussian induced dipole polarization model. J. Comput. Chem. 28: 1261-1274. PMID:17299773

S.M. Tschampel, M.R. Kennerty, R.J. Woods. 2007. A TIP5P-consistent treatment of electrostatics for biomolecular simulations. J. Chem. Theory Comput. 3: 1721-1733. PMID:25419191

S. Pedatella, M. De, B. Ernst, A. Guaragna, B. Wagner, R.J. Woods, G. Palumbo. 2007. New sialyI Lewis(x) mimic containing an alpha-substituted beta(3)-amino acid spacer. Carbohydr. Res. 343: 31-38. PMID:17980866

R. Kadirvelraj, M.L. Beckham, M.G. Ford, J. Gonzalez-Outeriño, R.J. Woods. 2006. Understanding the bacterial polysaccharide antigenicity of Streptococcus agalactiae versus Streptococcus pneumoniae. Proc. Natl. Acad. Sci. USA 103: 8149-8154. PMID:16705032

J. Gonzalez-Outeriño, K.N. Kirschner, S. Thobhani, R.J. Woods. 2006. Reconciling solvent effects on rotamer populations in carbohydrates: A joint MD and NMR analysis. Can. J. Chem. 84: 1-11.

S. Kawatkar, D.A. Kuntz, R.J. Woods, D.R. Rose, G.J. Boons. 2006. The structural basis of the inhibition of golgi a-mannosidase II by mannostatin A and the role of the thiomethyl moiety in protein ligand interactions. J. Am. Chem. Soc. 128: 8310-8319. PMID:16787095

J. Gonzalez, J.E. Gonzalez, R. Kadirvelraj, R.J. Woods. 2005. Structural elucidation of type III group B Streptococcus capsular polysaccharide using molecular dynamics simulations: The role of sialic acid. Carbohydr. Res. 340: 1007-1018. PMID:15780265

D.A. Case, T. Cheatham, T. Darden, H. Gohlke, R. Luo, K.H. Merz,, A. Onufriev, C. Simmerling, B.C. Wang, R.J. Woods. 2005. The AMBER biomolecular simulation programs. J. Comput. Chem. 26: 1668-1688. PMID:16200636

F. Corzana, M.S. Motawia, C. Herve, S. Perez, S.M. Tschampel, R.J. Woods, S.B. Engelsen. 2004. A hydration study of (1-4) and (1-6) linked a-glucans by comparative 10 ns molecular dynamics simulations and 500 MHz NMR. J. Comput. Chem. 25: 573-586. PMID:14735575

J. Gonzalez, J. Glushka, A. Siriwardena, R.J. Woods. 2004. The structure and conformational behavior of sulfonium salt glycosidase inhibitors in solution: A combined quantum mechanical-NMR approach. J. Am. Chem. Soc. 126: 6866-6867. PMID:15174846

C. Bosques, S.M. Tschampel, R.J. Woods, B. Imperiali. 2004. Effects of glycosylation on peptide conformation: A synergistic experimental and computational study. J. Am. Chem. Soc. 126: 8421-8425. PMID:15237998

B. Li, S.P. Kawatkar, G.S. Strachan, H. Strachan, R.J. Woods, A. Siriwardena, K.W. Moremen, G.J. Boons. 2004. Inhibition of Golgi mannosidase II with mannostatin A analogues: synthesis, biological evaluation, and structure-activity relationship studies. Chem. BioChem. 5: 1220-1227. PMID:15368573

T. Netherwoods, S.M. Martin-Orue, A.G. ODonnell, S. Gockling, J. Graham, J.C. Mathers, H.J. Gilbert. 2004. Assessing the survival of transgenic plant DNA in the human gastrointestinal tract. Nature Biotechnol. 22: 204-209. PMID:14730317

S.M. Tschampel, R.J. Woods. 2003. Quantifying the role of water in protein-carbohydrate interactions. J. Phys. Chem. 107: 9175-9181. PMID:16906231

M.G. Ford, T. Weimar, T. Kohli, R.J. Woods. 2003. Molecular dynamics simulations of galectin-1-oligosaccharide complexes reveal the molecular basis for ligand diversity. Proteins: Structure, Function & Genetics 53: 229-240. PMID:14517974

W. Tempel, S. Tschampel, R.J. Woods. 2002. The xenograft antigen bound to Griffonia simplicifolia isolectin 1B4: X-ray crystal structure of the complex and molecular dynamics characterization of the binding site. J. Biol. Chem. 277: 6615-6621. PMID:11714721

R. Bukowski, L.C. Morris, R.J. Woods, T. Weimar. 2001. Synthesis and conformational analysis of the T-antigen disaccharide b-D-Gal-(1->3)-b-D-GalNAc-Ome). Eur. J. Org. Chem. : 2697-2705.

K.N. Kirschner, R.J. Woods. 2001. A quantum mechanical study of the non-bonded forces in water-methanol complexes. J. Phys. Chem. A 105: 4150-4155. PMID:16518456

C. Clarke, R.J. Woods, A. Cooper, M.A. Nutley, G.-J. Boons. 2001. The involvement of water in carbohydrate-protein binding. J. Am. Chem. Soc. 123: 12238-12247. PMID:11734024

M. Basma, S. Sundara, D. Calgan, T. Varnali, R.J. Woods. 2001. Solvated ensemble averaging in the calculation of partial atomic charges. J. Comput. Chem. 22: 1125-1137.

K.N. Kirschner, R.J. Woods. 2001. Solvent interactions determine carbohydrate conformation. Proc. Natl. Acad. Sci. USA 98: 10541-10545. PMID:11526221

W. Tempel, L.A. Lipscomb, J.P. Rose, R.J. Woods. 2001. The xenograft antigen in complex with a GS-1B4 lectin: crystallization and preliminary X-ray analysis. Acta Crystallog. Section D. D57: 1639-1642. PMID:11679730

A. Pathiaseril, R.J. Woods. 2000. Relative energies of binding for antibody carbohydrate-antigen complexes computed from free-energy simulations. J. Am. Chem. Soc. 122: 331-338. PMID:17211491

H. Valafar, F. Valafar, A. Darvill, P. Albersheim, A. Kutlar, K.F. Woods, J. Hardin. 2000. Predicting the effectiveness of hydroxyurea in individual sickle cell anemia patients. Artificial Intell. Med. 18: 133-148.

R.J. Woods, R. Chappelle. 2000. RESP-partial charges for condensed phase MD simulations. J. Mol. Struct. (THEOCHEM). 527: 149-156.

R.J. Woods. 1998. Computational carbohydrate chemistry: what theoretical methods can tell us. Glycoconj. J. 15: 209-216. PMID:9579797

R.J. Woods, A. Pathiaseril, M.R. Wormald, C.J. Edge, R.A. Dwek. 1998. The high degree of internal flexibility observed for an oligomannose oligosaccharide does not alter the overall topology of the molecule. Eur. J. Biochem. 258: 372-386. PMID:9874202

J.-R. Brisson, S. Uhrinova, R.J. Woods, M. Van, H.C. Jarrell, L.C. Paoletti, D.L. Kasper, H.J. Jennings. 1997. NMR and molecular dynamics studies of the conformational epitope of the type-III group-B Streptococcus capsular polysaccharide and derivatives. Biochemistry 36: 3278-3292. PMID:9116006

P.M. Rudd, R.J. Woods, M.R. Wormald, G. Opdenakker, A.K. Downing, I.D. Campbell, R.A. Dwek. 1995. The effects of variable glycosylation on the functional activities of ribonuclease, plasminogen and tissue plasminogen activator. Biochem. Biophys. Acta 1248: 1-10. PMID:7711052

R.J. Woods. 1995. 3-Dimensional structures of oligosaccharides. Curr. Opin. Struct. Biol. 5: 591-598. PMID:8574693

R.J. Woods, R.A. Dwek, C.J. Edge, B. Fraser-Reid. 1995. Molecular mechanical and molecular dynamical simulations of glycoproteins and oligosaccharides. 1. GLYCAM_93 parameter development. J. Phys. Chem. 99: 3832-3846.

RJ Woods, CJ Edge, RA Dwek. 1994. Protein Surface Oligosaccharides and Protein Function. Nature, Struct Biol 1: 499-501. PMID:7664073

CJ Edge, HC Joao, RJ Woods, MR Wormald. 1993. The Conformational Effects of N-linked Glycosylation. Biochem Soc Trans 21: 452-455. PMID:8359508

RJ Woods, CW Andrews, JP Bowen. 1992. A Molecular Mechanical Investigation of the Properties of Oxocarbenium Ions. II Application to Glycoside Hydrolysis. J Am Chem Soc 114: 859-864.

RJ Woods, CW Andrews, JP Bowen. 1992. A Molecular Mechanical Investigation of the Properties of Oxocarbenium Ions I. Parameter Development. J Am Chem Soc 114: 850-858.

RJ Woods, WA Szarek, VH Smith Jr.. 1991. A Comparison of the Semiempirical and ab initio Methods for the Study of Structural Features of Relevance in Carbohydrate Chemistry. J Chem Soc, Chem Commun : 334-337.

RJ Woods, WA Szarek, VH Smith Jr.. 1991. A Comparison of the Semiempirical and ab initio Methods for the Study of Structural Features of Relevance in Carbohydrate Chemistry. J Chem Soc, Chem Commun : 334-337.

RJ Woods, WA Szarek, VH Smith Jr.. 1991. The Proton Affinities and Deprotonation Enthalpies of beta-D-fructopyranose and alpha-L-sorbopyranose: An Examination Using the Semiempirical Molecular Orbital Method, AM1. Can J Chem 69: 1917-1928.

M Khalil, RJ Woods, DF Weaver, VH Smith Jr. 1991. An Examination of Intermolecular and Intramolecular Hydrogen Bonding in Biomolecules by AM1 and MNDO/M Semiempirical Methodologies. J. Comput. Chem. 12: 584-593.

RJ Woods, WA Szarek, VH Smith Jr.. 1990. An Investigation of the Relationship Between Sweetness and Intra-molecular Hydrogen-bonding Networks in Hexuloses Using the Semi-empirical Molecular Orbital Method, Am1. J. Am. Chem. Soc. 112: 4732-4741.

RJ Woods, M Khalil, W Pell, SH Moffat, VH Smith Jr. 1990. Derivation of Net Atomic Charges from Molecular Electrostatic Potentials. J. Comput. Chem. 11: 297-310.

RJ Woods, KA Watson, S Fortier, WA Szarek. 1989. The Conformation of 6-tho-beta-D-ructopyranose in the Crystalline State. Carbohydrate Res 193: 1-7.

RJ Woods, VH Smith, WA Szarek, A Farazdel. 1987. Ab initio LCAO-MO Calculations on alpha-D-glucopyranose, beta-D-fructopyranose and their Thiopyranoid-ring Analogues. Application to a Theory of Sweetness.. J. Chem. Soc. Chem. Commun. : 937-939.

G Chalmers, JN Glushka, BL Foley, RJ Woods, JH Prestegard. 0. Direct NOE simulation from long MD trajectories. J Magn Reson 265: 1-9. PMID:26826977

S Makeneni, DF Thieker, RJ Woods. 0. Applying Pose lustering and MD Simulations to Eliminate False Positives in Molecular Docking. J. Chem. Inf. Model Submitted: -.

SA Flowers, OC Grant, RJ Woods, GW Rebeck. 0. O-glycosylation on Cerebrospinal Fluid and Plasma Apolipoprotein E Differs in the Lipid Binding Domain. Nat. Neurosci. Submitted: -.

M Pikoula, MB Tessier, RJ Woods, Y Ventikos. 0. Effect of Fluid Shear Stress on Orientation and Conformation Properties of Oligossacharides: Atomic-Scale Endothelial Glycocalyx Modelling. Submitted: -.

Book Chapters

R.J. Woods, A.B. Yongye. 2012. Computational Techniques Applied to Defining Carbohydrate Antigenicity. In: Anticarbohydrate Antibodies: From Molecular Basis to Clinical Application (Eds. P. Kosma and S. Muller-Loennies), pp. Chapter 15. Springer, Wien, Austria.

R.J. Woods. 1998. Carbohydrate force fields. In: Encyclopedia of Computational Chemistry(P.V.R. Schleyer, N.L. Allinger, T. Clark, J. Gasteiger, P.A. Kollman, H.F. Schaefer III, P.R. Schreiner, eds.), Vol.Vol. 1:220-233. Chichester: John Wiley & Sons..

R.J. Woods. 1996. The application of molecular modeling techniques to the determination of oligosaccharide solution conformations. In: Reviews in Computational Chemistry, Vol. 9 (K. Lipkowitz and D.B. Boyd, eds.), pp. 129-165. VCH Publishers, New York.

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