Peer Reviewed Journals

Woods, R.J., Smith,V.H.JR., Szarek,W.A., Farazdel,A. (1987) 'Ab initio LCAO-MO calculations on ?-D-glucopyranose, ?-D-fructopyranose, and their thiopyranoid-ring analogues Application to a theory of sweetness'. J. Chem. Soc.; Chem. Commun, (937):334-337. [Details]

Woods, R.J., Watson,K.A., Fortier,S., Szarek,W.A. (1989) 'The conformation of 6-thio-?-D-fructopyranose in the crystalline state'. Carbohydrate Res, 193 :1-7. [Details]

Woods, R.J., Khalil,M., Pell,W., Moffat,S.H., Smith,V.H.Jr. (1990) 'Derivation of net atomic charges from molecular electrostatic potentials'. J. Comput. Chem, 11 :297-310. [Details]

Khalil, M., Woods,R.J., Weaver,D.F, Smith,V.H Jr. (1990) 'An examination of intermolecular and intramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical methodologies'. J. Comput. Chem, 12 :584-593. [Details]

Woods, R.J., Szarek,W.A., Smith,V.H.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. [Details]

Woods, R.J., Szarek,W.A., Smith,V.H. 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. [Details]

Woods, R.J., Szarek,W.A., Smith,V.H.Jr. (1991) 'The proton affinities and deprotonation enthalpies of ?-D-fructopyraonse and ?-L-sorbopyranose: An examination using the semiempirical molecular orbital method, AM1'. Can. J. Chem, 69 :1917-1928. [Details]

Woods, R.J., Rews,C.W., Bowen,J.P. (1992) 'A molecular mechanical investigation of the properties of oxocarbenium ions I Parameter development'. J. Am. Chem. Soc, 114 :850-858. [Details]

Woods, R.J., Rews, C.W., Bowen,J.P. (1992) 'A molecular mechanical investigation of the properties of oxocarbenium ions II Application to glycoside hydrolysis'. J. Am. Chem. Soc, 114 :859-864. [Details]

Edge, C.J., Joao,H.C., Woods,RJ., Wormald,M.R. (1993) 'The conformational effects of N-linked glycosylation'. Biochem. Soc. Trans, 21 :452-455. [Details]

Woods, R.J., Edge,C.J., Dwek,R.A. (1994) 'Protein surface oligosaccharides and protein function'. Nature, Struct. Biol, 1 :499-501. [Details]

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

Woods, R.J. (1995) '3-Dimensional structures of oligosaccharides'. Curr. Opin. Struct. Biol, 5 :591-598. [Details]

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

Brisson, J.-R, Uhrinova, S, Woods, R.J, Van Der Zwan,M, Jarrell,H.C, Paoletti,L.C, Kasper,D.L, Jennings,H.J. (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. [Details]

Woods, R.J. (1998) 'Computational carbohydrate chemistry: What theoretical methods can tell us'. Glycoconj. J, 15 :209-216. [Details]

Woods, R.J., Pathiaseril,A., Wormald,M.R., Edge,C.J., Dwek,R.A. (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. [Details]

Woods, R.J., Chappelle,R. (2000) 'RESP-partial charges for condensed phase MD simulations'. J. Mol. Struct. THEOCHEM, 22 :149-156. [Details]

Clarke, C., Woods,R.J., Cooper,A., Nutley,M.A., Boons,G.J. (2001) 'The involvement of water in carbohydrate-protein binding'. J. Am. Chem. Soc, 123 :12238-12247. [Details]

Basma, M, Sundara,S, Calgan,D, Varnali,T, Woods,R.J. (2001) 'Solvated ensemble averaging in the calculation of partial atomic charges'. J. Comput. Chem, (22):1125-1137. [Details]

Bukowski, R, Morris,L, Woods,R.J, Weimar,T. (2001) 'Synthesis and conformational analysis of the T-antigen disaccharide'. Eur. J. Org. Chem, :2697-2705. [Details]

Kirschner, K.N., Woods,R.J. (2001) 'A quantum mechanical study of the non-bonded forces in water-methanol complexes'. J. Phys. Chem. A, 4 :4150-4155. [Details]

Tempel, W., Lipscomb,L.A., Rose,J.P., Woods,R.J. (2001) 'The xenograft antigen in complex with a GS-1-B4 lectin: crystallization and preliminary X-ray analysis'. Acta Crystallog, (D57):1639-1642. [Details]

Kirschner, K., Woods,R.J. (2001) 'Solvent interactions determine carbohydrate conformation'. Proc. Natl. Acad. Sci. USA 98, :10541-10545. [Details]

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

Tschampel, S.M., Woods,R.J. (2003) 'Quantifying the role of water in protein-ligand interactions'. J. Phys. Chem. A, 107 :9175-9181. [Details]

Ford, M.G, Weimar,T, Köhli,T, Woods,R.J. (2003) 'MD simulations of galectin-1 -- Oligosaccharide complexes reveal the molecular basis for ligand diversity'. Proteins: Structure, Function and Genetics, 53 :229-240. [Details]

Bosques, C, Tschampel,S.M, Woods,R.J, Imperiali,B. (2004) 'Effects of glycosylation on peptide conformation: a synergistic experimental and computational study'. J. Am. Chem. Soc, 126 :8421-8425. [Details]

Gonzalez Outeriño, J., Glushka,J., Siriwardena,A., Woods,R.J. (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. [Details]

Corzana, F, Motawia,M.S, C. Hervé du Penhoat,Perez,S, Tschampel,S.M, Woods,R.J, Engelsen,S.B. (2004) 'A hydration study of 1-4) and 1-6) linked ?-glucans by comparative 10 ns molecular dynamics simulations and 500 MHz NMR'. J. Comput. Chem, 25 :573-586. [Details]

Case, D.A., Cheatham, T, Darden,T, Gohlke,H, Luo,R, Merz,K.H, Onufriev,A, Simmerling,C, Wang,B, Woods,R.J. (2005) 'The AMBER biomolecular simulation programs'. J. Comput. Chem, 26 :1668-1688. [Details]

Gonzalez Outeriño, J., Kadirvelraj,R., Woods,R.J. (2005) 'Structural elucidation of type III group B Streptococcus capsular polysaccharide using molecular dynamics simulations: the role of sialic acid'. Carbohydr. Res, :1007-1018. [Details]

Li, B., Kawatkar,S., George, S., Strachan,H., Woods,R.J., Siriwardena, A., Moremen,K.W., Boons,G.J. (2005) 'Inhibition of golgi mannosidase II with mannostatin A analogues: synthesis, biological evaluation, and structure activity relationship studies'. Chembiochem, :1220-1227. [Details]

Kawatkar, S.P., Kuntz, D.A., Woods, R.J., Rose, D.R., Boons, G.J. (2006) 'Structural basis of the inhibition of golgi ?-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions'. J. Am. Chem. Soc, 128 :8310-8319. [Details]

Woods, R. (2006) 'Understanding the bacterial polysaccharide antigenicity of Streptococcus agalactiae versus Streptococcus pneumoniae'. Proc. Natl. Acad. Sci, 103 :8149-8154. [Details]

Gonzalez-Outeiriño, J.,Kirschner,K.N.,Thobhani,S.,Woods,R.J. (2006) 'Reconciling solvent effects on rotamer populations in carbohydrates: a joint MD and NMR analysis'. Can. J. Chem, 84 :569-579. [Details]

Elking, D., Darden,T., Woods,R.J. (2006) 'Gaussian induced dipole polarization model'. J.Comput. Chem, 28 :1261-1274. [Details]

Seyfried, N. T., Atwood,J.A., Almond, A., Day,A.J., Orlo, R., Woods,R.J. (2007) 'Fourier transform mass spectrometry to monitor hyaluronan-protein interactions: use of hydrogen/deuterium amide exchange, Rapid Commun'. Mass Spectrom, 21 :121-131. [Details]

Tschampel, S. M., Kennerty,M.R., Woods,R.J. (2007) 'A TIP5P-Consistent Treatment of Electrostatics for Biomolecular Simulations'. J. Chem. Theory Comput, 3 :1721-1733. [Details]

Kirschner,K.N., Yongye,A.B., Tschampel,S.M., Gonzalez Outeriño,J., Daniels,C.R., Foley,B.L., Woods,R.J. (2008) 'GLYCAM06: A Generalizable Biomolecular Force Field: Carbohydrates'. J. Comput. Chem, 29 :622-655. [Details]

DeMarco, M.L , Woods,R.J. (2008) 'Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer, and its implications for ganglioside-protein recognition at membrane surfaces Glycobiology Submitted'. . [Details]

Yongye,A.B, Foley,B.L, Woods,R.J. (2008) 'On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol'. J. Phys. Chem. A, 112 :2634-2639. [Details]

Seo,M., Castillo,N., Ganzynkowicz, R., Daniels,C.R., Woods,R.J., Roy,R.N., Lowary,T.L. (2008) 'An approach for the simulation and modeling of flexible rings  Application to the α-D-arabinofuranoside ring, a key constituent of polysaccharides from Mycobacterium tuberculosis'. J. Chem. Theory Comput, 4 :184-191. [Details]

DeMarco,M.L., Woods,R.J. (2008) 'Structural Glycobiology: A Game of Snakes and Ladders'. Glycobiology Invited Review), 18 :426-440. [Details]

Charvatova, O, Foley,B.L, Bern,M, Sharp,J, Orlo,R, Woods,R.J. (2008) 'Quantifying Protein Interface Footprinting by Hydroxyl Radical Oxidation and Molecular Dynamics Simulation: Application to Galectin-1'. J. Am. Soc. Mass Spectrom. In Press, . [Details]

Tessier,M.B., DeMarco,M.L., Yongye,A.B., Woods,R.J. (2008) 'Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids'. Molecular Simulation, 34 :349-364. [Details]

Kadirvelraj, R., Foley,B.L., Dyekjær,J.D., Woods,R.J. (2008) 'Involvement of Water in Carbohydrate-Protein Binding: Concanavalin A Revisited'. J. Am. Chem. Soc. In Press, . [Details]

DeMarco, M.L , Woods,R.J. (2008) 'Bridging Structural Biology and Glycobiology: A Game of Snakes and Ladders Invited Review)'. Glycobiology, 18 :426-440. [Details]

Yongye, A.B., Gonzalez-Outeriño,J., Glushka,J., Schutlheis,V., Woods,R.J. (2008) 'The Conformational Properties of Methyl a-2,8)- di/trisialoside Implications for anti-Neisseria meningitidis Vaccine Design'. Biochemistry, . [Details]

Charvatova, O., Foley, B.L., Bern,M., Sharp, J., Orlo,R., Woods,R.J. (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. [Details]

Kadirvelraj,R., Foley,B.L., Dyekjær,J.D,, Woods,R.J. (2008) 'Involvement of Water in Carbohydrate-Protein Binding: Concanavalin A Revisited'. J. Am. Chem. Soc, 130 :16933-16942. [Details]

Demarco, M.I., Woods,R.J. (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 (4). [Details]

Watson,C., Janik, I., Zhuang, T., Charvatova, O., Woods, R.J., Sharp, J.S. (2009) 'Pulsed electron beam water radiolysis for submicrosecond hydroxyl radical protein footprinting'. Analytical Chemistry, 81 (7). [Details]

Woods,R.J., Tessier, M.B. (2010) 'Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan-protein complexes'. Current Opinion in Structural Biology, 20 (5). [Details]

DeMarco, M.L., Woods, R.J., Prestegard, J.H., Tian, F. (2010) 'Presentation of membrane-anchored glycosphingolipids determined from molecular dynamics simulations and NMR paramagnetic relaxation rate enhancement'. Journal of the American Chemical Society, 132 (4). [Details]

Woods,R.J.., Tessier,M. (2010) 'Computational Glycoscience: Characterizing the Spatial and Temporal Properties of Glycans and Glycan-Protein Complexes'. Curr. Opin. Struct. Biol, 20 :1-9. [Details]

Fadda, E., Woods, R.J. (2010) 'Molecular simulations of carbohydrates and protein-carbohydrate interactions: Motivation, issues and prospects'. Drug Discovery Today, 15 (15-16). [Details]

Kadirvelraj,R., Grant, O.C., Goldstein, I.J., Winter, H.C., Tateno, H., Fadda, E., Woods, R.J. (2011) 'Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Ac2-6Gal1-4GlcNAc human-type influenza receptor'. Glycobiology, 21 (7):973-984. [DOI] [Details]

Ju,R., Tessier, M., Olliff, L., Woods, R., Summers, A., Geng, Y. (2011) 'Supramolecular dendrimer capsules by cooperative binding'. Chemical Communications, 47 (1). [Details]

                                       

Workshops

Woods, R.J. (2002) Computational carbohydrate chemistry: Strengths, weaknesses and future prospects. 223rd American Chemical Society National Meeting, Orlando, Florida. Workshops [Details]

Woods, R.J. (2003) Computational Carbohydrate Chemistry: Water, Water, Everywhere. University of Alberta, Department of Chemistry. Workshops [Details]

Woods, R.J. (2003) Computational Carbohydrate Chemistry: Water, Water, Everywhere. Gordon Research Conference Carbohydrates. Workshops [Details]

Woods, R.J., Kirschner,K.N., Gonzales-Outeriño,J. (2003) Computational Carbohydrate Chemistry: Water, Water, Everywhere . 43rd Sanibel Symposium. Workshops [Details]

Woods, R.J. (2003) Modeling Carbohydrates with the GLYCAM Force Field . AMBER/CHARMM Developers Meeting. Workshops [Details]

Woods, R.J. (2004) Computational Carbohydrate Chemistry: The Interface Between Theory and Experiment. ACS Spring Meeting. Workshops [Details]

Woods, R.J. (2004) Enhancing Computational Modeling and Simulation with Itanium Technology. HP Itanium Webcast. Workshops [Details]

Woods, R.J. (2004) Glycam Web Development and Glycoprotein Force Field. AMBER Developers Meeting. Workshops [Details]

Woods, R.J. (2004) A structural Model for the Antigenicity of Group B Streptococcus Type III. Carbohydrate Moieties as Vaccine Candidates Meeting, NIH, Bethesda, MD. Workshops [Details]

Woods, R.J. (2005) Understanding Antigenicity: Streptococcus agalactiae Group B Streptococcus) versus S pneumoniae. NIH, Bethesda, MD. Workshops [Details]

Woods, R.J. (2005) Understanding Antigenicity: Streptococcus agalactiae Group B Streptococcus) versus S pneumoniae. Wyeth Pharmaceuticals. Workshops [Details]

Woods, R.J. (2005) Linux in the Life Sciences. Linux World Convention. Workshops [Details]

Woods, R.J. (2005) Integrating Computation and Experiment in Determining Carbohydrate Structure-Function Relationships. National University of Ireland. Workshops [Details]

Woods, R.J. (2005) Computational Tools for Understanding Carbohydrate Antigenicity: Streptococcus agalactiae Group B Streptococcus) versus S pneumoniae. Annual Society for Glycobiology Meeting. Workshops [Details]

Woods, R.J. (2005) A Structural Model for the Antigenicity of Type III Group B Streptococcus. University of Toronto. Workshops [Details]

Woods, R.J. (2005) A structural model for the antigenicity of group B Streptococcus Type III: the influence of sialylation on antigen conformation and affinity. 13th European Carbohydrate Symposium. Workshops [Details]

Woods, R.J. (2005) A Structural Model for the Antigenicity of Type III Group B Streptococcus. Gordon Research Conference Carbohydrates. Workshops [Details]

Woods, R.J. (2005) Glycam Web Development and Glycoprotein Force Field. AMBER Developers Meeting. Workshops [Details]

Woods, R.J. (2006) Evolution of a Polarizable TIP5P-Consistent Force Field. Gordon Research Conference Carbohydrates), Les Diablarets. Workshops [Details]

Woods, R.J. (2006) Evolution of a Polarizable TIP5P-Consistent Force Field. International Conference of Computational Methods in Sciences and Engineering. Workshops [Details]

Woods, R.J. (2006) Computational simulations in glycobiology: linking structure and function. ACS Spring Meeting. Workshops [Details]

Woods, R.J. (2006) Understanding Carbohydrate Antigenicity: Group B Streptococcus type III versus S pneumoniae type 14. IBC's 17th Annual International Conference Antibody Engineering. Workshops [Details]

Woods, R.J. (2006) 3D Structure Prediction Tools for Glycoscience: From Monosaccharides to Glycoproteins. Frontiers in Glycomics, NIH. Workshops [Details]

Woods, R.J. (2006) Molecular dynamics simulations of the endopolygalacturonase II - octagalacturonate complex. ACS Spring Meeting. Workshops [Details]

Woods, R.J. (2006) Probing 3D Structure-Function Relationships in Glycobiology. Interdisciplinary Translational Glycobiology, Biodesign Center. Workshops [Details]

Woods, R.J. (2006) Structure and Dynamics of Polysaccharides and Polysaccharide-Protein Complexes. FASEB Meeting on Microbial Polysaccharides of Medical, Agricultural and Industrial Importance. Workshops [Details]

Woods, R.J. (2007) Computational Simulations in Glycoscience: Predicting Carbohydrate Affinity and Antigenicity. Emerson Center Lectureship Award Symposium. Workshops [Details]

Woods, R.J. (2007) Computational Docking and Free Energy Calculations applied to Carbohydrate-Protein Interactions. Frontiers in Macromolecular Simulation. Workshops [Details]

Woods, R.J. (2007) Computational Simulation: Applied to Structure-Affinity Predictions. La Jolla Biotechnology Institute. Workshops [Details]

Woods, R.J. (2007) Understanding Bacterial Polysaccharide Antigenicity- What Makes Sugar Stick?. Swiss Federal Institute of Technology ETH. Workshops [Details]

Woods, R.J. (2007) Computational Docking and Free Energy Calculations applied to Carbohydrate-Protein Interactions. Center for Theoretical and Biological Physics. Workshops [Details]

Woods, R.J. (2007) Computational Simulations in Glycoscience: Predicting Carbohydrate Affinites and Carbohydrate-Protein Structures. Annual Glycobiology Society Meeting. Workshops [Details]

Woods, R.J. (2007) Computational Simulations in Glycoscience: Predicting Carbohydrate Affinites and Carbohydrate-Protein Structures. I2CAM Exploratory Workshop Glycome: Structure to Disease. Workshops [Details]

Woods, R.J. (2007) Computational Glycoscience: Probing Structure-Function Relationships. 10th Annual San Diego Glycobiology Symposium. Workshops [Details]

Woods, R.J. (2007) Quantum-Derived Force Fields for Classical Dynamics Simulations of Biomolecules. Swiss Federal Institute of Technology ETH. Workshops [Details]

Woods, R.J. (2007) Combining X-ray and Computational Data to Model Prokaryotic N-Glycoproteins. National Research Council of Canada. Workshops [Details]

Yongye, A., Woods, R.J. (2007) Computational tools employed in carbohydrate vaccine design. NIH Workshop on carbohydrate moieties as vaccine antigens, Bethesda, MD. Workshops [Details]

Woods, R.J. (2008) Computationally-guided Glycoscience: Predicting the Structures and Energies of Carbohydrate-Protein Interactions. Workshop & Ph.D. course: Biomolecular Interactions by Computational Chemistry Tools. National Centre for Biomolecular Research. Brno. Workshops [Details]

Woods, R.J. (2008) Computational Simulations in Glycoscience: Predicting Affinities and Carbohydrate-Protein Structures. Computational Biophysics with Chemical Accuracy, Antigua. Workshops [Details]

Woods, R.J. (2008) Issues in modeling carbohydrate-protein interactions: toward virtual high-throughput glycan array screening. NIH Workshop. Workshops [Details]

Woods, R.J. (2008) Creation and Implementation of Virtual 3D Glycan Arrays. Consortium for Functional Glycomics Advisory Committee Meeting, Ft. Worth, TX. Workshops [Details]

Woods, R.J. (2008) GLYCAM06, a generalizable biomolecular force field: Carbohydrates, lipids, lipid bilayers and glycolipids. 235th ACS Spring Meeting. Workshops [Details]

Woods, R.J. (2008) Computational Prediction of Influenza Receptor Specificity. Virtual Discovery, Europe. Workshops [Details]

Woods, R.J. (2008) Understanding Carbohydrate Antigenicity: All Epitopes are Conformational. Case Western Reserve University School of Medicine. Workshops [Details]

Woods, R.J. (2008) Characterizing Carbohydrate-Protein Interactions from the Protein Perspective. AICCS 4th National Carbohydrate Symposium. Workshops [Details]