Source: https://www.h-its.org/de/forschung/mcm/publikationen/
Timestamp: 2019-04-26 10:33:18+00:00

Document:
Structure (2019), in press, DOI: 10.1016/j.str.2019.01.003 (Abstract).
Accelerating Drug Discovery Efforts for Trypanosomatidic Infections Using an Integrated Transnational Academic Drug Discovery Platform.
SLAS DISCOVERY: Advancing Life Sciences R&D (2019), 24(3), 346–361, DOI: 10.1177/2472555218823171 (Fulltext).
Influence of Transmembrane Helix Mutations on Cytochrome P450-Membrane Interactions and Function.
Biophysical Journal (2019), 16(3):419 – 432, DOI: 10.1016/j.bpj.2018.12.014 (Fulltext).
Molecular Modeling in Drug Design.
Molecules (2019), 24(2):321, Editorial for Special Issue “Molecular Modeling in Drug Design”, DOI: 10.3390/molecules24020321 (Fulltext).
A genetic screen pinpoints ribonucleotide reductase residues that sustain dNTP homeostasis and specifies a highly mutagenic type of dNTP imbalance.
Nucleic Acids Research (2019), 47(1):237-252, DOI: 10.1093/nar/gky1154 (Fulltext).
The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing.
PLoS Pathogens (2018), 14(9):e1007315, DOI: 10.1371/journal.ppat.1007315 (Fulltext).
ACS Medicinal Chemistry Letters (2018), 9(11):1134-1139, DOI: 10.1021/acsmedchemlett.8b00397 (Fulltext).
Toward an Ensemble View of Chromatosome Structure: A Paradigm Shift from One to Many.
Structure (2018), 26(8):1050-1057, DOI: 10.1016/j.str.2018.05.009 (Fulltext).
Equilibrium Model of Drug-Modulated GagPol-Embedded HIV-1 Reverse Transcriptase Dimerization to Enhance Premature Protease Activation.
AIDS Res. Hum. Retroviruses (2018), 34(9):804-807, DOI: 10.1089/aid.2018.0111 (Fulltext).
MCMap—A Computational Tool for Mapping Energy Landscapes of Transient Protein–Protein Interactions.
ACS Omega (2018), 3(6):6465-6475, DOI: 10.1021/acsomega.8b00572 (Fulltext).
PLOS Biology (2018), 16(7):e2005345, DOI: 10.1371/journal.pbio.2005345 (Fulltext).
Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations.
J. Chem. Theory Comput. (2018), 14(7):3859-3869 DOI: 10.1021/acs.jctc.8b00230 (Fulltext).
Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification.
Biophys. J. (2018), DOI: 10.1016/j.bpj.2018.04.034 (Fulltext).
Halogenaromatische π-Wechselwirkungen Modulieren Die Verweilzeit von Inhibitoren.
Angew. Chem. (2018), 130(24):7338–7343, DOI: 10.1002/ange.201801666 (Abstract).
Halogen‐aromatic π‐interactions modulate inhibitor residence time.
Angew. Chem. Int. Ed. (2018), 57(24):7220-7224, DOI: 10.1002/anie.201801666 (Abstract).
Computing Protein-Ligand Binding Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics Simulations.
Impact of carbonylation on glutathione peroxidase-1 activity in human hyperglycemic endothelial cells.
Redox Biology (2018), 16:113-122, DOI: 10.1016/j.redox.2018.02.018 (Fulltext).
New approaches for computing ligand–receptor binding kinetics.
Current Opinion in Structural Biology (2018), 49:1-10, DOI: 10.1016/j.sbi.2017.10.001 (Fulltext).
Drosophila melanogaster linker histone (dH1) binding to the nucleosome.
In “Proceedings of the 3rd bwHPC Symposium: Heidelberg 2016”, Eds: Richling, S., Baumann, M., Heuveline, V., HeiBOOKS (2017) pp 100-102. (Fulltext).
Nature Communications (2017), 8(1):2276, DOI: 10.1038/s41467-017-02258-w (Fulltext).
A novel homozygous ARL13B variant in patients with Joubert syndrome impairs its guanine nucleotide-exchange factor activity.
European Journal of Human Genetics (2017), 25:1324–1334, DOI:10.1038/s41431-017-0031-0 (Abstract).
Comparative mapping of on-targets and off-targets for the discovery of anti-trypanosomatid folate pathway inhibitors.
Biochim Biophys Acta (BBA) – General Subjects (2017), 1861(12): 3215–3230, DOI: 10.1016/j.bbagen.2017.09.012 (Abstract).
ACS Omega (2017), 2(9): 5666-5683, DOI:10.1021/acsomega.7b00473 (Fulltext).
Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition.
J Comput Aided Mol Des. (2017), 31(8): 715-728. DOI:10.1007/s10822-017-0035-4 (Fulltext).
Kinetics for Drug Discovery: an industry-driven effort to target drug residence time.
Drug Discovery Today (2017), 22(6):896-911 (Abstract).
A unique profilin-actin interface is important for malaria parasite motility.
PLoS Pathog (2017), 13(5): e1006412 (Fulltext).
TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.
Nucleic Acids Res (2017), 45(W1):W325-W330, (Fulltext).
Pöhner, I.A., Panecka, J. and Wade, R.C.
What determines docking performance in drug discovery? A case study of PTR1, an anti‑parasitic target.
Journal of Cheminformatics (2016), 8(Suppl 1):P46 (Meeting Abstracts).
Reaction-diffusion basis of retroviral infectivity.
Philos. Transactions Royal Soc. Lond. A: Math. Phys. Eng. Sci. (2016), 374:2080, (Abstract).
Human DPP III – Keap1 Interactions: A Combined Experimental And Computational study.
Croat. Chem. Acta (2016), 89(2), DOI: 10.5562/cca2916, (Fulltext).
Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties.
Proteins: Structure, Function, and Bioinformatics (2016), 84:1844-1858, (Abstract).
Global profiling of SRP interaction with nascent polypeptides.
An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association.
J. Chem. Theory Comput. (2016), 59:7598-7616, (Abstract).
J. Med. Chem. (2016), 59:7598-7616, (Abstract).
Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets.
J. Chem. Theory Comput. (2016), 12:4100–4113, (Fulltext).
Nucl. Acids Res. (2016), 44:6599-6613, (Fulltext).
J. Mol Biol. (2016), 428:2880-2897, (Abstract).
ProSAT+: visualizing sequence annotations on 3D structure.
Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen.
J. Phys. Chem. (2016), 120:8580-8589, (Abstract).
Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.
Acc. Chem. Res. (2016), 49:809-815, (Fulltext).
Three steps to gold: Mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations.
Phys Chem Chem Phys. (2016) 18:10191-200, (Fulltext).
The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration.
Nat. Commun. (2016) 7:10764, (Abstract).
Xiaofeng Yu, Daria B. Kokh, Prajwal Nandekar, Ghulam Mustafa, Stefan Richter, Rebecca C. Wade.
Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer.
In “High Performance Computing in Science and Engineering ’15: Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2015”, Eds. Nagel, E. Wolfgang; Kröner, H. Dietmar; Resch, M. Michael. Springer International Publishing, Cham, Switzerland, (2016) pp. 255-264, (Abstract).
Rafiullah Rafiullah, Muhammad Aslamkhan, Nagarajan Paramasivam, Christian Thiel, Ghulam Mustafa, Stefan Wiemann, Matthias Schlesner, Rebecca C. Wade, Gudrun A. Rappold and Simone Berkel.
Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family.
J. Med. Genetics. (2016) 53:138-144, (Abstract).
Musa Ozboyaci, Daria B. Kokh, Stefano Corni and Rebecca C. Wade.
Modeling and simulation of protein–surface interactions: achievements and challenges.
Quart Rev Biophys (2016) 49, e4, (Fulltext).
Khalid Mohammed Khan, Mohammad A. Mesaik, Omer M. Abdalla, Fazal Rahim, Samreen Soomro, Sobia A. Halim, Ghulam Mustafa, Nida Ambreen, Ahmad Shukralla Khalid, Muhammad Taha, Shahnaz Perveen, Muhammad Tanveer Alam, Abdul Hameed, Zaheer Ul-Haq, Hayat Ullah, Zia Ur Rehman, Rafat Ali Siddiqui and Wolfgang Voelter.
The immunomodulation potential of the synthetic derivatives of benzothiazoles: Implications in immune system disorders through in vitro and in silico studies.
Bioorg. Chem. (2016) 64:21-28, (Abstract).
Xiaofeng Yu, Prajwal Nandekar, Ghulam Mustafa, Vlad Cojocaru, Galina I. Lepesheva and Rebecca C. Wade.
Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design.
Biochim. Biophys. Acta (BBA) – General Subjects , (2016) 1860:67-78, (Abstract).
Marta Rosa, Daria B. Kokh, Stefano Corni, Rebecca Wade and Rosa Di Felice.
Docking of DNA Duplexes on a Gold Surface.
J. Self-Assembly and Molecular Electronics (SAME), (2015) 3(7): 1-18, DOI: 10.13052/jsame2245-4551.2015009, (Fulltext).
Ghulam Mustafa, Prajwal P. Nandekar, Xiaofeng Yu and Rebecca C. Wade.
J. Chem. Phys., (2015) 143:243139, (Abstract).
Divita Garg, Stephane Skouloubris, Julien Briffotaux, Hannu Myllykallio and Rebecca C. Wade.
Conservation and Role of Electrostatics in Thymidylate Synthase.
Sci. Rep., (2015) 5:17356, (Abstract).
Julia Romanowska, Daria B. Kokh, and Rebecca C. Wade.
When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces.
Nano Lett., (2015) 15:7508-7513, (Abstract).
Antonija Tomić, Mykhaylo Berynskyy, Rebecca C. Wade and Sanja Tomić.
Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding.
Mol. BioSyst., (2015) 11:3068-3080, (Abstract).
A multiscale approach to simulating the conformational properties of unbound multi-C2H2 zinc finger proteins.
SDA 7: A modular and parallel implementation of the simulation of diffusional association software.
J. Comput. Chem., (2015) 36:1631-1645, (Fulltext).
Molecular identification and functional characterization of the first Nα-acetyltransferase in plastids by global acetylome profiling.
Kar1 binding to Sfi1 C-terminal regions anchors the SPB bridge to the nuclear envelope.
J. Cell Biol., (2015) 209:843-861, (Fulltext).
Xiaofeng Yu, Michael Martinez, Annika L. Gable, Jonathan C. Fuller, Neil J. Bruce, Stefan Richter and Rebecca C. Wade.
Nucl. Acids Res., (2015) 43:W220-W224, (Fulltext).
Outi M. H. Salo-Ahen, Anna Tochowicz, Cecilia Pozzi, Daniela Cardinale, Stefania Ferrari, Yap Boum, Stefano Mangani, Robert M. Stroud, Puneet Saxena, Hannu Myllykallio, Maria Paola Costi, Glauco Ponterini and Rebecca C. Wade.
J. Med. Chem., (2015) 58:3572-3581, (Fulltext).
N.J. Bruce, Daria B. Kokh, M. Ozboyaci and Rebecca C. Wade.
Modelling of solvation effects for brownian dynamics simulation of biomolecular recognition.
In “Computational Trends in Solvation and Transport in Liquids-Lecture Notes, IAS Series, Schriften des Forschungszentrums Jülich”, Eds. Sutmann G, Grotendorst J, Gommpper G, Marx D. Forschungszentrum Jülich GmbH, Jülich, Germany (2015), vol. 28, pp. 259-280. (Fulltext).
Julia Romanowska, Daria B. Kokh, Jonathan C. Fuller and Rebecca C. Wade.
Computational Approaches for Studying Drug Binding Kinetics.
In “Kinetics and Thermodynamics of Drug Binding Kinetics and Thermodynamics of Drug Binding”, Eds. Keserü GM, Swinney DC. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, (2015) vol. 65, pp. 7508-7513. (Fulltext).
Xiaofeng Yu, Vlad Cojocaru, Ghulam Mustafa, Outi M. H. Salo-Ahen, Galina I. Lepesheva and Rebecca C. Wade.
Dynamics of CYP51: implications for function and inhibitor design.
J. Molec. Recogn., (2015) 28:59-73. (Fulltext).
Jonathan C. Fuller, Michael Martinez, Stefan Henrich, Antonia Stank, Stefan Richter and Rebecca C. Wade.
Paolo Mereghetti, Michael Martinez and Rebecca C. Wade.
BMC Biophysics, (2014) 7(1):4. (Fulltext).
Jonathan C. Fuller, Michael Martinez and Rebecca C. Wade.
On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate-Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics.
PLOS ONE, (2014) 9(8):e104778. (Fulltext).
Ghulam Mustafa, Xiaofeng Yu and Rebecca C. Wade.
Structure and Dynamics of Human Drug-Metabolizing Cytochrome P450 Enzymes.
In Drug Metabolism Prediction, (2014) pages 75-102. Wiley-VCH Verlag GmbH & Co. KGaA. (Fulltext).
Linda Gombos, Annett Neuner, Mykhaylo Berynskyy, Luca L. Fava, Rebecca C. Wade, Carsten Sachse and Elmar Schiebel.
GTP regulates the microtubule nucleation activity of γ-tubulin.
Nat Cell Biol., (2013) 15:1317-27. (Abstract).
Arzu Sandikci, Felix Gloge, Michael Martinez, Matthias P. Mayer, Rebecca Wade, Bernd Bukau and Guenter Kramer.
Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding.
Nat Struct Mol Biol., (2013) 20:843-50. (Abstract).
Nadine Veith, Anna Feldman-Salit, Vlad Cojocaru, Stefan Henrich, Ursula Kummer and Rebecca C Wade.
Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria.
PLoS Comput Biol., (2013) 9:e1003159. (Fulltext).
Anna Feldman-Salit, Silvio Hering, Hanan L Messhia, Nadine Veith, Vlad Cojocaru, Antje Sieg, Hans V. Westerhoff, Bernd Kriekemeyer, Rebecca C Wade and Tomas Fiedler.
Regulation of the Activity of Lactate Dehydrogenases from Four Lactic Acid Bacteria.
J. Biol. Chem., (2013) 288:21295-306. (Abstract).
Daria B Kokh, Stefan Richter, Stefan Henrich, Paul Czodrowski, Friedrich Rippmann and Rebecca C Wade.
TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins.
J. Chem Inf Model, (2013) 53:1235-52. (Abstract).
Jessica Balbo, Paolo Mereghetti, Dirk-Peter Herten and Rebecca C Wade.
The Shape of Protein Crowders is a Major Determinant of Protein Diffusion.
Biophys. J., (2013) 104:1576-84. (Abstract).
Paolo Mereghetti and Rebecca C. Wade.
Brownian dynamics simulation of protein diffusion in crowded environments.
AIP Conf. Proc., (2013) 1518:511-516. (Abstract).
Xiaofeng Yu, Vlad Cojocaru and Rebecca C. Wade.
Biotechnology and Applied Biochemistry, (2013) 60:134-45. (Fulltext).
Divita Garg, Alexander V. Beribisky, Glauco Ponterini, Alessio Ligabue, Gaetano Marverti, Andrea Martello, M. Paola Costi, Michael Sattler and Rebecca C. Wade.
Translational repression of thymidylate synthase by targeting its mRNA.
Nucleic Acids Res., (2013) 41 (7): 4159-4170. (Fulltext).
Mykhaylo Berynskyy and Rebecca C. Wade.
Treating conformational flexibility in protein-protein docking.
Curr. Phys. Chem., (2013) 3:27-35. (Fulltext).
Stefania Ferrari, Marco Ingrami, Fabrizia Soragni, Rebecca C. Wade and M. Paola Costi.
Ligand-based discovery of N-(1,3-dioxo-1H,3H-benzo[de]isochromen-5-yl)-carboxamide and sulfonamide derivatives as thymidylate synthase A inhibitors.
Bioorg Med Chem Lett., (2013) 23:663-8. (Abstract).
Yuki Oguchi, Eva Kummer, Fabian Seyffer, Mykhaylo Berynskyy, Benjamin Anstett, Regina Zahn, Rebecca C Wade, Axel Mogk and Bernd Bukau.
A tightly regulated molecular toggle controls AAA+ disaggregase.
Nat Struct Mol Biol., (2012) 19:1338-46. (Abstract).
Giorgia Brancolini, Daria B. Kokh, Luigi Calzolai, Rebecca C. Wade and Stefano Corni.
Docking of Ubiquitin to Gold Nanoparticles.
ACS Nano, (2012) 6:9863-78. (Abstract).
Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions.
J. Phys. Chem. B, (2012) 116:8523-8533. (Abstract).
Lada Biedermannová, Zbynek Prokop, Artur Gora, Eva Chovancova, Mihaly Kovacs, Jiri Damborsky and Rebecca C. Wade.
A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB.
J. Biol. Chem., (2012) 287:29062-74. (Abstract).
Matthias Stein, Manohar Pilli, Sabine Bernauer, Bianca H. Habermann, Marino Zerial and Rebecca C. Wade.
The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity.
PLoS ONE, (2012) 7:e34870. (Fulltext).
Anna Feldman-Salit, Markus Wirtz, Esther D. Lenherr, Christian Throm, Michael Hothorn, Klaus Scheffzek, Rüdiger Hell and Rebecca C. Wade.
Vlad Cojocaru, Peter J. Winn and Rebecca C. Wade.
Multiple, Ligand-dependent Routes from the Active Site of Cytochrome P450 2C9.
Curr. Drug. Metab., (2012) 13:143-154. (Abstract).
Daniela Cardinale, Giambattista Guaitoli, Donatella Tondi, Rosaria Luciani, Stefan Henrich, Outi M. H. Salo-Ahen, Stefania Ferrari, Gaetano Marverti, Davide Guerrieri, Alessio Ligabue, Chiara Frassineti, Cecilia Pozzi, Stefano Mangani, Dimitrios Fessas, Remo Guerrini, Glauco Ponterini, Rebecca C. Wade and Maria Paola Costi.
Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase.
Proc. Natl. Acad. Sci. USA, (2011) 108:13889-13890, E542-E549. (Fulltext).
Vlad Cojocaru, Kia Balali-Mood, Mark S. P. Sansom and Rebecca C. Wade.
PLoS Comput. Biol., (2011) 7(8):e1002152. (Fulltext) ; (Cover Figure).
Outi M.H. Salo-Ahen and Rebecca C. Wade.
The active-inactive transition of human thymidylate synthase: Targeted molecular dynamics simulations.
Diffusion of hydrophobin proteins in solution and interactions with a graphite surface.
BMC Biophysics, (2011) 4:9. (Fulltext).
Sundar Raman S., R. Gopalakrishnan, Rebecca C. Wade and V. Subramanian.
Structural Basis for the Varying Propensities of Different Amino Acids To Adopt the Collagen Conformation.
J. Phys. Chem. B., (2011) 115:2593-2607. (Abstract).
Daria B. Kokh, Rebecca C. Wade and Wolfgang Wenzel.
WIREs Comput. Molec. Sci., (2011) 1:298-314. (Fulltext).
Paolo Mereghetti, Daria B. Kokh, J. Andrew McCammon and Rebecca C. Wade.
Diffusion and association processes in biological systems: theory, computation and experiment.
BMC Biophysics, (2011) 4:2. (Fulltext).
Georgi V. Pachov, Razif R. Gabdoulline and Rebecca C. Wade.
On the structure and dynamics of the complex of the nucleosome and the linker histone.
Nucl. Acid. Res., (2011) 39 (12): 5255-5263. (Fulltext).
Stefania Ferrari, Federica Morandi, Domantas Motiejunas, Erika Nerini, Stefan Henrich, Rosaria Luciani, Alberto Venturelli, Sandra Lazzari, Samuele Calo, Shreedhara Gupta, Veronique Hannaert, Paul A. M. Michels, Rebecca C. Wade and M. Paola Costi.
Virtual Screening Identification of Nonfolate Compounds, Including a CNS Drug, as Antiparasitic Agents Inhibiting Pteridine Reductase.
J. Med. Chem., (2011) 54:211-221. (Abstract).
Ori Cohavi, Dana Reichmann, Renne Abramovich, Alexander B. Tesler, Giuliano Bellapadrona, Daria B. Kokh, Rebecca C. Wade, Alexander Vaskevich, Israel Rubinstein and Gideon Schreiber.
A Quantitative, Real-Time Assessment of Binding of Peptides and Proteins to Gold Surfaces.
Chem. Eur. J., (2011) 17:1327-1336. (Abstract).
Sandeep Kaur-Ghumaan, Lennart Schwartz, Reiner Lomoth, Matthias Stein and Sascha Ott.
Katalytische Wasserstofferzeugung an einem einkernigen Eisen(II)-Carbonylkomplex als kleinstes funktionelles Modell für das aktive Zentrum von [FeFe]-Hydrogenasen.
Angew. Chem., (2010) 122:8207-8211. (Abstract).
Catalytic Hydrogen Evolution from Mononuclear Iron(II) Carbonyl Complexes as Minimal Functional Models of the [FeFe] Hydrogenase Active Site.
Angew. Chem. Intl., (2010) 49:8033-8036. (Abstract).
Simone Loescher, Antje Gebler, Matthias Stein, Oliver Sanganas, Thorsten Buhrke, Ingo Zebger, Holger Dau, Baerbel Friedrich, Oliver Lenz and Michael Haumann.
Protein–Protein Complex Formation Affects the Ni–Fe and Fe–S Centers in the H2-Sensing Regulatory Hydrogenase from Ralstonia eutropha H16.
Chem. Phys. Chem., (2010) 11:1297-1306. (Abstract).
Markus Wirtz, Hannah Birke, Corinna Heeg, Christopher Mueller, Fabian Hosp, Christian Throm, Anna Feldman-Salit, Karsten Rippe, Gabriele Petersen, Rebecca C. Wade, Vladimir Rybin, Klaus Scheffzek and Ruediger Hell.
J. Biol. Chem., (2010) 285:32810-32817. (Abstract).
Paolo Mereghetti, Razif R. Gabdoulline and Rebecca C. Wade.
Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties.
Biophys. J., (2010) 99:3782-3791. (Abstract).
Divita Garg, Stefan Henrich, Outi M. H. Salo-Ahen, Hannu Myllykallio, Maria P. Costi and Rebecca C. Wade.
Novel Approaches for Targeting Thymidylate Synthase To Overcome the Resistance and Toxicity of Anticancer Drugs.
J. Med. Chem., (2010) 53:6539-6549. (Abstract).
Edda Klipp, Rebecca C. Wade and Ursula Kummer.
Curr. Op. Biotech., (2010) 21:511-516. (Abstract).
Daria B. Kokh, Stefanio Corni, Peter J. Winn, Martin Hoefling, Key E. Gottschalk and Rebecca C. Wade.
ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent.
J. Chem. Theory Comput., (2010) 6:1753-1768. (Abstract).
Sean I. O’Donoghue, David S. Goodsell, A. S. Frangakis, F. Jossinet, Roman A. Laskowski, Michael Nilges, Helen R. Saibil, Andrea Schafferhans, Rebecca C. Wade, Eric Westhof and Art J. Olson.
Nature Methods, (2010) 7:42-55. (Abstract).
Olivier Michielin and Rebecca C. Wade.
Foreword preface to the jmr special issue on ‘dynamic aspects of molecular recognition’.
J. Mol. Recogn., (2010) 23:101. (Abstract).
Daniela Cardinale, Outi M.H. Salo-Ahen, Stefania Ferrari, Glauco Ponterini, G. Crucicali, E. Carotati, Anna Tochowicz, Stefano Mangani, Rebecca C. Wade and M. Paola Costi.
Homodimeric enzymes as drug targets.
Curr. Med. Chem., (2010) 17:826-846. (Abstract).
Daniela Cardinale, Outi M.H. Salo-Ahen, G. Guatoli, Stefania Ferrari, Alberto Venturelli, Silvia Franchini, R. Battini, Rebecca C. Wade and M. Paola Costi.
Design and characterization of a mutation outside the active site of human thymidylate synthase that affects ligand binding.
Prot. Eng. Des. Sel., (2010) 23:81-89. (Abstract).
Matthias Stein, Razif R. Gabdoulline and Rebecca C. Wade.
Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields.
Mol. BioSyst., (2010) 6:162-174. (Abstract).
Ori Cohavi, Stefano Corni, Francesca De Rienzo, Rosa Di Felice, Kay E. Gottschalk, Martin Hoefling, Daria Kokh, Elisa Molinari, Gideon Schreiber, Alexei Vaskevich and Rebecca C. Wade.
Protein-surface interactions: challenging experiments and computations.
J. Mol. Recogn., (2010) 23:259-262. (Abstract).
Kinetics of biomacromolecular complex formation: Theory and experiment.
In ” Protein-Protein Complexes: Analysis, Modeling and Drug Design”, Ed. M. Zacharias, World Scientific/Imperial College Press, (2010) pages 89-119. Contents.
Stefan Henrich, Outi M.H. Salo-Ahen, Bingding Huang, Friedrich F. Rippmann, Gabriele Cruciani and Rebecca C. Wade.
Computational approaches to identifying and characterizing protein binding sites for ligand design.
J. Mol. Recogn., (2010) 23:209-219. (Abstract).
Stefan Henrich, Isabella Feierberg, Ting Wang, Niklas Blomberg and Rebecca C. Wade.
metapocket: a meta approach to improve protein ligand binding sites prediction.
Christian Müller, Maria Antonia Gomez-Zurita Frau, Dario Ballinari, Sonia Colombo, Alessandro Bitto, Enzo Martegano, Cristina Arnold, Anske Stephanie van Neuren, Matthias Stein, Jörg Weiser, Carlo Battistini and Francesco Peri.
Design, synthesis, and biological evaluation of levoglucosenome-derived ras activation inhibitors.
Pradyuma S. Singh, Hans C. Rudbeck, Ping Huang, Salah Ezzaher, Lars Eriksson, Matthias Stein, Sascha Ott and Reiner Lomoth.
(i,0) mixed-valence state of a diiron complex with pertinence to the [fefe]-hydrogenase active site: An ir, epr, and computational study.
Inorganic Chemistry, (2009) 48:10883-10885. (Abstract).
Martina Pavlova, Martin Klvana, Zbynek Prokop, Radka Chaloupkova, Pavel Banas, Michal Otyepka, Rebecca C. Wade, Masataka Tsuda, Yuji Nagata and Jiri Damborsky.
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.
Nature Chem. Biol., (2009) 5:727-733. (Abstract).
Martin Klvana, Martina Pavlova, Tana Koudelakova, Radka Chaloupkova, Pavel Dvorak, Alena Stsiapanava, Michal Kuty, Ivana Kuta-Smatanova, Jan Dohnalek, Petr Kulhanek, Rebecca C. Wade and Jiri Damborsky.
Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations.
J. Mol. Biol., (2009) 392:1339-1356. (Abstract).
Razif R. Gabdoulline and Rebecca C. Wade.
On the contributions of diffusion and thermal activation to electron transfer between phormidium laminosum plastocyanin and cytochrome f: Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events.
J. Am. Chem. Soc., (2009) 131:9230-9238. (Abstract).
Computational simulations of protein-protein and protein-nucleic acid association.
In ” Computational Protein-Protein Interactions”, Eds. R. Nussinov and G. Schreiber, Taylor and Francis Group LLC, Boca Raton, (2009) pages 109-128.
Georgi V. Pachov and Rebecca C. Wade.
Docking of a linker histone to the nucleosome with flexible linker dnas.
Biophys. J., (2009) 96:83a-84a. (Abstract).
Daria B. Kokh, Bingding Huang, Rebecca C. Wade and Peter J. Winn.
Modeling of protein adsorption on a metal surface: Brownian dynamics simulations.
Biophys. J., (2009) 96:298a-299a. (Abstract).
Anna Feldman-Salit, Markus Wirtz, Ruediger Hell and Rebecca C. Wade.
Anna Feldman-Salit and Rebecca C. Wade.
Molecular recognition, computation and modeling of.
In Encyclopedia of Chemical Biology. Wiley. (Link).
Woelkart K., Salo-Ahen O. M. and Bauer R.
CB receptor ligands from plants.
Curr Top Med Chem., (2008) 8(3):173-86. (Abstract).
Curr Top Med Chem., (2008) 8(3):172.
J. Hegermann, S. Halbedel, R. Dumke, J. Regula, R.R. Gabdoulline, F. Mayer, J. Stuelke and R. Herrmann.
The acidic, glutamine-rich mpn474 protein of mycoplasma pneumoniae is surface exposed and covers the complete cell.
Stefan Richter, Anne Wenzel, Matthias Stein, Razif R. Gabdoulline and Rebecca C. Wade.
Nucleic Acids Res., (2008) 36:W276-80. (Fulltext).
A. Weidemann, S. Richter, M. Stein, S. Sahle, R. Gauges, R. Gabdoulline, I. Surovtsova, N. Semmelrock, B. Besson, I. Rojas, R. Wade and U. Kummer.
SYCAMORE-a systems biology computational analysis and modeling research environment.
Heidrun Witan, Andreas Kern, Ingrid Koziollek-Drechsler, Rebecca Wade, Christian Behl and Albrecht M. Clement.
Human Molecular Genetics, (2008) 17:1373-1385. (Abstract).
Domantas Motiejunas, Razif R. Gabdoulline, Ting Wang, Anna Feldman-Salit, Tim Johann, Peter J. Winn and Rebecca C. Wade.
Protein-protein docking by simulating the process of association subject to biochemical constraints.
Calculating enzyme kinetic parameters from protein structures.
Biochem. Soc. Trans., (2008) 36:51-54. (Abstract).
Branimir Bertosa, Biserka Kojic-Prodic, Rebecca C. Wade and Sanja Tomic.
Mechanism of auxin interaction with auxin binding protein (ABP1): a molecular dynamics simulation study.
Stefan Henrich, Stefan Richter and Rebecca C. Wade.
On the use of PIPSA to guide target-selective drug design.
Eilers G., Schwartz L., Stein M., Zampella G., de Gioia L., Ott S. and Lomoth R.
Ligand versus metal protonation of an iron hydrogenase active site mimic.
Chemistry., (2007) 13 (25):7075-84. (Fulltext).
Simone Loescher, Lennart Schwartz, Matthias Stein, Sascha Ott and Michael Haumann.
Facilitated hydride binding in an fe-fe hydrogenase active?site biomimic revealed by x-ray absorption spectroscopy and dft calculations.
Inorg. Chem., (2007) 46 (26):11094-11105. (Fulltext).
Razif R. Gabdoulline, Matthias Stein and Rebecca C. Wade.
qPIPSA: Relating enzymatic kinetic parameters and interaction fields.
BMC Bioinformatics, (2007) 8:373. (Fulltext).
Bridging from molecular simulation to biochemical networks.
Curr. Op. Struct. Biol., (2007) 17:166-172. (Abstract).
Exploring biomolecular recognition by modelling and simulation.
In Modeling and Simulation in Science. Proceedings of the 6th International Workshop on Data Analysis in Astronomy “Livio Scarsi”, (2007) pages 150-153. Eds. V. Di Gesu, G. Lo Bosco and M.C. Maccarone., World Scientific Publishing Co..
Georgi Pachov, Razif R. Gabdoulline and Rebecca C. Wade.
Simulation of linker histone-chromatin interactions.In ‘From Computational Biophysics to Systems Biology (CBSB2007)’, John von Neumann Institute for Computing, Juelich, NIC Series 36:69-74. (Fulltext).
Ting Wang and Rebecca C. Wade.
On the use of elevated temperature in simulations to study protein unfolding mechanisms.
J. Chem. Theory Comput., (2007) 3:1476-1483. (Abstract).
Peter J. Winn, Mai Zahran, James N.D. Battey, Yanxiang Zhou, Rebecca C. Wade and Amit Banerjee.
Structural and electrostatic properties of ubiquitination and related pathways.
Frontiers in Bioscience, (2007) 12:3419-3430. (Abstract).
Sanja Tomic, Branimir Bertosa, Ting Wang and Rebecca C. Wade.
Peter J .Winn, Mai Zahran and Rebecca C. Wade.
Comparisons of the protein electrostatic potentials as a means to understanding function.
In Workshop on Protein Folding and Drug Design, (2007) volume 165 of Proceedings of the International School of Physics “Enrico Fermi”, (2007) pages 207-219. Eds. Broglia, R.A., Serrano, L., Tiana, G., Societa Italiana di Fisica, Bologna, Italy. ISBN 978-1-58603-792-5.
Andrey Karyakin, Domantas Motiejunas, Rebecca C. Wade and Christiane Jung.
FTIR studies of the redox partner interaction in cytochrome P450. the Pdx-P450cam couple.
Biochimica et Biophysica Acta. General Subjects, (2007) 1770:420-431 . (Abstract).
Matthias Stein, Razif R. Gabdoulline, Bruno Besson and Rebecca C. Wade.
The estimation of kinetic parameters in systems biology by comparing molecular interaction fields of enzymes.
In Beilstein Proceedings of the 2nd Conference on Experimental Standard Conditions of Enzyme Characterizations,Ruedesheim, 19-23 March, 2006, (2007) pages 237-253. (Fulltext).
The ins and outs of cytochrome P450s.
Biochimica et Biophysica Acta. General Subjects, (2007) 1770:390-401 . (Abstract).
Domantas Motiejunas and Rebecca C. Wade.
Structural, energetic, and dynamic aspects of ligand-receptor interactions.
In Comprehensive Medicinal Chemistry II, (2007) volume 4, pages 193-213. Eds. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford.
Gabriele Cruciani, Emanuele Carosati, Rebecca C. Wade and Massimo Baroni.
Characterization of protein-binding sites and ligands using molecular interaction fields.
In Comprehensive Medicinal Chemistry II, (2007) volume 4, pages 237-253. Eds. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford.
Integrating structural and kinetic enzymatic information in systems biology.In NIC Workshop 2006 ‘From Computational Biophysics to Systems Biology’,6-9 June, John von Neumann Institute for Computing, Juelich, volume 34 of NIC Series, (2006) pages 129-132. (Abstract & Full Text).
Schleinkofer K., Wang T. and Wade R.C.
In Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, (2006) pages pp1149-1153. Ed. Ganten,D. and Ruckpaul, K. Springer.
Razif R. Gabdoulline, Stefan Ulbrich, Stefan Richter and Rebecca C. Wade.
Nucl. Acids. Res., (2006) 34:W79-W83. (Abstract & Full Text).
Henrik R. Hallingbaeck, Razif R. Gabdoulline and Rebecca C. Wade.
Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking.
Alexander Spaar, Christian Dammer, Razif R. Gabdoulline, Rebecca C. Wade and Volkhard Helms.
Diffusional encounter of barnase and barstar.
Biophys. J., (2006) 90:1913-1924. (Abstract).
Force field effects on a beta-sheet protein domain structure in thermal unfolding simulations.
J. Chem. Theory Comput., (2006) 2:140-148. (Abstract).
Karl J. Jalkanen, Vibeke Würtz-Jürgensen, Anetta Claussen, Abdoul Rahim, G. M. Jensen, Rebecca C. Wade, Frederico Nardi, Christiane Jung, Ivan M. Degtyarenko, Risto M. Nieminen, Frank Herrmann, Michaela Knapp-Mohammady, Thomas A. Niehaus, Kenneth Frimand and Sandor Suhai.
Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach.
Intl. J. Quant. Chem., (2006) 106:1160-1198. (Abstract).
Rebecca C. Wade, Domantas Motiejunas, Karin Schleinkofer, Peter J. Winn Sudarko, Amit Banerjee, Andrei Kariakin and Christiane Jung.
Multiple molecular recognition mechanisms. cytochrome P450-a case study.
Biochimica et Biophysica Acta, (2005) 1754:239-244. (Abstract).
Calculation and application of molecular interaction fields.
In Molecular Interaction Fields. Applications in Drug Discovery and ADME Prediction, (2005) pages Ch. 2, pp27-42. Ed. Cruciani, G., Wiley-VCH Weinheim, ISBN 3-527-31087-8. (Publisher Link).
J. Andrew McCammon and Rebecca C. Wade.
Pushing the limits: Editorial overview.
Curr. Opin. Struct. Biol., (2005) 15:135-136. (Link).
Karin Schleinkofer, Peter J. Winn Sudarko, Susanna K. Lüdemann and Rebecca C. Wade.
EMBO Reports, (2005) 6:584-589. (Abstract).
J. Mol. Recognit., (2005) 18:191. (Link).
Jan Kmunicek, Kamila Hynkova, Tomas Jedlicka, Yuji Nagata, Ana Negri, Federico Gago, Rebecca C. Wade and Jiri Damborsky.
Peter J. Winn, James N. Battey, Karin Schleinkofer, Amit Banerjee and Rebecca C. Wade.
Issues in high-throughput comparative modelling: A case study using the ubiquitin E2 conjugating enzymes.
Lutz P. Ehrlich, Michael Nilges and Rebecca C. Wade.
The impact of protein flexibility on protein-protein docking.
Rebecca C. Wade, Stefan Henrich and Ting Wang.
Using 3D protein structures to derive 3D-QSARs.
Drug Discovery Today: Technologies, (2004) 1(3):241-246. (Abstract).
Karin Schleinkofer, Urs Wiedemann, Livia Otte, Ting Wang, Gerd Krause, Hartmut Oschkinat and Rebecca C. Wade.
J. Mol. Biol., (2004) 344:865-881. (Abstract).
Peter J. Winn, Tomasz L. Religa, James D. Battey, Amit Banerjee and Rebecca C. Wade.
Determinants of functionality in the ubiquitin conjugating enzyme family.
Structure, (2004) 12:1563-74. (Abstract) ; (The Ubiquitin and Ubiquitin-like Protein Web Resource).
Ting Wang, Sanja Tomic, Razif R. Gabdoulline and Rebecca C. Wade.
Biophys. J., (2004) 87:1618-1630. (Abstract).
Francesca De Rienzo, Razif R. Gabdoulline, Rebecca C. Wade, Marco Sola and M Cristina Menziani.
Computational approaches to structural and functional analysis of plastocyanin and other blue copper proteins.
Cell Mol. Life Sci, (2004) 61:1123-1142. (Abstract).
Rebecca C. Wade, Peter J. Winn, Ilme Schlichting and Sudarko.
J. Inorg. Biochem., (2004) 98:1175-1182. (Abstract).
Jiri Damborsky, Jan Kmunicek, Tomas Jedlicka, Santos Luengo, Federico Gago, Angel R. Ortiz and Rebecca C. Wade.
Rational re-design of haloalkane dehalogenases guided by comparative binding energy analysis.
I (2004)n Enzyme functionality: Design, Engineering and Screening pages pp79-96. Ed. A. Svendsen, Marcel Dekker, New York. ISBN: 0-8247-4709-7.
Tomasz Zemojtel, Rebecca C. Wade and Thomas Dandekar.
In search of the prototype of nitric oxide synthase.
FEBS Letts., (2003) 554:1-5. (Abstract).
Stefania Ferrari, M. Paola Costi and Rebecca C. Wade.
Inhibitor specificity via protein dynamics: Insights from design of antibacterial agents targeted against thymidylate synthase.
Chemistry & Biology, (2003) 10:1183-1193. (Abstract).
Branimir Bertosa, Biserka Kojic-Prodic, Rebecca C. Wade, Michael Ramek, Stavroula Piperaki, Anna Tsantili-Kakoulidou and Sanja Tomic.
A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: Application to auxins.
Chem. Inf. Comput. Sci., (2003) 43:1532-1541. (Abstract).
Timm Essigke, G. Matthias Ullmann and Rebecca C. Wade.
What determines the redox potential of ferredoxins?
In “Proceedings of the 13th International Conference on Cytochromes P450″, (2003) pages 25-30. Monduzzi Editore, Bologna .
Jan Kmunicek, Michal Bohac, Santos Luengo, Federico Gago, Rebecca C. Wade and Jiri Damborsky.
J. Comput. Aided Mol. Des., (2003) 17:299-311. (Abstract).
Razif Gabdoulline, Rebecca C. Wade and Dirk Walther.
MolSurfer: a macromolecular interface navigator.
Nucleic Acids Res., (2003) 31:3349-3351. (Abstract) ; (Fulltext) ; (Webserver).
Razif Gabdoulline, Ursula Kummer, Lars F. Olsen and Rebecca C. Wade.
Concerted simulations reveal how peroxidase compound III formation results in cellular oscillations.
Biophys. J., (2003) 85:1421-1428. (Fulltext) ; (Movie).
Razif Gabdoulline, Rene Hoffmann, Florian Leitner and Rebecca C. Wade.
ProSAT: Functional annotation of protein 3D structures.
Bioinformatics, (2003) 19:1723-1725. (Abstract) ; (Webserver).
Giacomo Finocchiaro, Ting Wang, Rene Hoffmann, Aitor Gonzalez and Rebecca C.
DSMM – a database of simulated molecular motions.
Nucleic Acids Res., (2003) 31:456-457. (Abstract) ; (Fulltext) ; (Database).
Eric Deprez, Edward Gill, Volkhard Helms, Rebecca C. Wade and Gaston Hui Bon Hoa.
Specific and non-specific effects of potassium cations on substrate-protein interactions in cytocromes P450cam and P450lin.
J. Inorg. Biochem., (2002) 91:597-606. (Abstract).
Comparative binding energy (COMBINE) analysis of OppA-peptide complexes.
Med. Chem., (2002) 45:4828-4837. (Abstract).
Peter J. Winn, Susanna K. Lüdemann, Ralph Gauges, Valere Lounnas and Rebecca C. Wade.
Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a new functional role for a buried arginine.
Proc. Natl. Acad. Sci. USA, (2002) 99:5361-5366. (Abstract) ; (Full text).
Curr. Opin. Struct. Biol., (2002) 12:204-213. (Abstract).
Amit Banerjee and Rebecca C. Wade.
Elusive recognition determinants for ubiquitination.
J. Molec. Recogn., (2002) 15:3-5. (Abstract).
Francesca De Rienzo, Razif R. Gabdoulline, Rebecca C. Wade and M. Cristina Menziani.
Biologically relevant properties of copper-containing proteins analysed by means of semi-quantitative and quantitative theoretical descriptors.
In Handbook of Copper Pharmacology and Toxicology, (2002) pages pp. 53-80. Ed. E. J. Massaro, Humana Press, Totowa, New Jersey.
De Rienzo, F., Gabdoulline,R.R., Menziani,M.C., De Benedetti, P.G. and Wade,R.C.
Biophys. J. (2001) 81, 3090-3104.
Kmunicek, J., Luengo,S., Gago,F., Ortiz, A.R., Wade,R.C. and Damborsky,J.
Biochemistry (2001) 40, 8905-8917, 11288.
J. Med. Chem. (2001) 44, 961-971.
J. Mol. Biol. (2001) 306, 1139-1155.
Luedemann,S.K., Gabdoulline, R.R., Lounnas,V. and Wade,R.C.
Wade,R.C., Gabdoulline, R.R. and De Rienzo, F.
Intl. J. Quant. Chem. (2001) 83, 122-127.
Croat. Chem. Acta. (2001) 74, 295-314.
Rev. Comp. Chem. (2001) 17, 61-97.
Jalkanen,K.J., Nieminen,R.M., Frimand,K., Bohr,J., Bohr, H., Wade,R.C., Tajkhorshid, E. and Suhai,S.
Chem. Phys. (2001) 265, 125-151.
In “Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships” Eds. Holtje, H-D., Sippl,W. (2001), Prous Science S.A., Barcelona, pp78-82.
In “Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships” Eds. Holtje, H-D., Sippl,W. (2001), Prous Science S.A., Barcelona, pp23-28.
Luedemann,S.K., Lounnas, V. and Wade, R.C.
How do substrates enter and products exit the buried active site of cytochrome P450cam ?
J. Mol. Biol. (2000) 303, 797-811.
J. Mol. Biol. (2000) 303, 813-830.
Das, B., Helms,V., Lounnas, V. and Wade, R.C.
De Rienzo, F., Gabdoulline,R.R., Menziani,M.C. and Wade,R.C.
Protein Science (2000) 9, 1439-54.
Nardi,F., Kemmink,J., Sattler,M. and Wade,R.C.
J. Biomol. NMR (2000) 17, 63-77.
Lamotte-Brasseur,J., Dubus, A. and Wade,R.C.
J. Med. Chem. (2000) 43, 1780-1792.
Eds. Gundertofte K. and Jorgensen F. S.
Plenum (2000), Kluwer Academic/Plenum Publishers, New York, 269-270.
Trends in Biochem. Sci. (1999) 24, 285-287.
Blomberg,N., Gabdoulline,R.R., Nilges,M. and Wade,R.C.
Nielsen,J.E., Andersen,K.V., Honig,B., Hooft,R.W.W., Klebe,G., Vriend,G. and Wade,R.C.
Protein Eng (1999) 12, 657-662.
J. Biomol. NMR (1999) 15, 169-172.
Elcock,A.H., Gabdoulline,R.R., Wade,R.C. and McCammon,J.A.
J. Mol. Biol. (1999) 291, 149-162.
J. Mol. Recogn. (1999) 12, 226-234.
Biophys. J. (1999) 77, 2191-2198.
J. Am. Chem Soc. (1999), 121, 3004 – 3014.
Biophys. Chem. (1999) 78, 157-182.
Lamotte-Brasseur,J., Lounnas,V., Raquet,X. and Wade,R.C.
pKa calculations for class A beta-lactamases: influence of substrate binding.
Protein Sci (1999) 8, 404-409.
Elsevier Science: Amsterdam, Netherlands (1999), Ch. 21, 859-898.
Knapp-Mohammady,M., Jalkanen,K.J., Nardi,F., Wade,R.C., Suhai,S.
Chemical Physics (1999) 240, 63-77.
Ringrose,L., Lounnas,V., Ehrlich,L., Buchholz,F., Wade,R.C., Stewart,F.A.
Journal of Molecular Biology (1998) 284, 363-384.
J. Phys. Chem. (1998) 32, 6260-6272.
Wade,R.C., Gabdoulline,R.R., Luedemann,S.K. and Lounnas,V.
Proc. Natl. Acad. Sci. USA (1998) 95, 5942-5949, (and colloquium cover illustration).
Tomic,S., Gabdoulline,R.R., Kojic-Prodic,B. and Wade,R.C.
Internet J. Chem. (1998) 1, 26.
Biophys. J. (1998) 74, 2906-2911.
J. Am. Chem. Soc. (1998) 120, 2710-2713.
Proteins (1998) 31, 406-416, (and cover illustration).
Madura,J.D., Briggs,J.M., Wade,R.C. and Gabdoulline,R.R.
Eds. Schleyer,P.v.R., Allinger,N.L., Clark,T., Gasteiger,J., Kollman,P.A. and Schaefer,H.F., Schreiner,P.R.
John Wiley & Sons: Chichester, UK, (1998) 1, 141-154.
J. Comput. Aided Mol. Des. (1998) 12, 63-79.
Ehrlich,L., Reczko,M., Bohr,H. and Wade,R.C.
Protein Eng. (1998) 11, 11-19.
Perspectives in Drug Discovery and Design (1998) 9, 19-34.
Eds. Kubinyi,H., Folkers,G. and Martin,Y.
Kluwer Academic Publishers, Dordrecht, The Netherlands. (1998).
in “Experimental and Computational Approaches in Structure Based Drug Design”, Ed. P. W. Codding, NATO ASI Series, Kluwer, Dortrecht (1998) 41-52.
Wade,R.C., Sobolev,V., Ortiz,A.R. and Peters,G.
in “Experimental and Computational Approaches in Structure Based Drug Design”, Ed. P. W. Codding, NATO ASI Series, Kluwer, Dortrecht (1998) 223-232.
Raquet,X.,Lounnas,V., Lamotte-Brasseur,J., Frere,J.M. and Wade,R.C.
Biophys. J. (1997) 73, 2416-2426.
Sobolev,V., Moallem,T.M., Wade,R.C., Vriend,G. and Edelman,M.
Proteins (1997) Suppl 1, 210-214.
J. Mol. Model. (1997) 3, 369-374.
Folding & Design (1997) 2, S62-68.
Biophys. J. (1997) 72, 1917-1929, (and cover illustration).
Ortiz,A.R., Pastor, M., Palomer,A., Cruciani,G., Gago,F. and Wade,R.C.
J. Med. Chem. (1997) 40, 1136-1148, 4168.
J. Comp. Chem. (1997) 18, 449-462.
J. Mol. Graph. (1996) 14, 341-353.
J. Phys. Chem. (1996) 100, 17373-17387.
Schulze,H., Hui Bon Hoa,G., Helms,V., Wade,R.C. and Jung,C.
Wade,R.C., Lounnas,V., Helms,V.,Hui Bon Hoa,G., Di Primo,C., Deprez,E., Barret,C., Kozin,S., Jung,C., Schulze,H., Contzen,J., Mouro,C., Gill,E., Simonneaux,G., Bondon,A., LeGrand,N. and Schlichting,I.
In “Perspectives on Protein Engineering” (Ed. M.J. Geisow), 3, BIODIGM, Nottingham (1996).
J. Mol. Graph. (1996) 14, 173-182, 146-147.
Peters,G.H., Olsen,O.H., Svendsen,A. and Wade,R.C.
Biophys. J. (1996) 71, 119-129.
In “Proceedings of the Third International Workshop on Parallel Algorithms for Irregularly Structure Problems”, Eds. Ferreira,A., Rolim,J., Saad,Y. and Yang, T., Springer, (1996) Lecture Notes in Computer Science, 1117, 313-318.
Sobolev,V., Wade,R.C., Vriend,G. and Edelman,M.
J. Phys. Chem. (1996) 100, 3868-3878.
Helms,V., Deprez,E., Gill,E., Barret,C., Hui Bon Hoa,G. and Wade,R.C.
Biochem. Soc. Trans. (1996) 24, 254-259.
Ortiz,A.R., Pisabarro,M.T., Gago,F. and Wade,R.C.
J.R. Prous Science Publishers, Barcelona, (1995) pp439-443.
J. Phys. Chem. (1995) 99, 17473-17482.
Acta Bioch. Polon. (1995) 42, 419-425.
J. Mol. Mod. (1995) 1, 93.
Madura,J.D., Briggs,J.M., Wade,R.C., Davis,M.E., Luty,B.A., Ilin,A., Antosiewicz,J., Gilson,M.K., Bagheri,B., Scott, L.R. and McCammon,J.A.
Comp. Phys. Comm. (1995) 91, 57-95.
Biophys. J. (1995) 69, 810-824.
J. Med. Chem. (1995) 38, 2681-2691.
Madura,J.D., Davis,M.E., Gilson,M.K., Wade,R.C., Luty,B.A. and McCammon,J.A.
Comp. Chem. Rev. (1994) 5, 229-267.
Pisabarro,M.T., Palomer,A., Ortiz,A.R., Wade,R.C., Gago,F., Mauleon,D. and Carganico,G.
of a Human Synovial Fluid Phospholipase A2 Inhibitor Leading to Enhanced Activity.
J. Mol. Graph. (1994) 12, 72.
Wade,R.C., Luty,B.A., Demchuk,E., Madura,J.D., Davis,M.E., Briggs,J.M. and McCammon,J.A.
Nature Struct. Biol. (1994) 1, 65-69.
Pisabarro,M.T., Ortiz,A.R., Palomer,A., Cabre,F., Garcia,L., Wade,R.C., Gago,F., Mauleon,D. and Carganico,G.
J. Med. Chem. (1994) 37, 337-341.
Demchuk,E., Mueller,T., Oschkinat,H., Sebald, W. and Wade,R.C.
Protein Science (1994) 3, 920-935, (and cover illustration).
Pisabarro,M.T., Ortiz,A.R., Serrano,L. and Wade,R.C.
Luty,B.A., Wade,R.C., Madura,J.D., Davis,M.E., Briggs,J.M. and McCammon,J.A.
J. Phys. Chem. (1993) 97, 233-237.
Wade,R.C., Davis,M.E., Luty,B.A., Madura,J.D. and McCammon,J.A.
Biophys. J. (1993) 64, 9-15.
Energetically Favorable Binding Sites on Molecules of Known Structure.
J. Med. Chem. (1993) 36, 140-147.
J. Med. Chem. (1993) 36, 148-156.
Demchuk,E., Vihinen,M., Wade,R. and Korpela,T.
Modeling three-dimensional structure and electrostatics of alkali-stable cyclomaltodextrin glucanotransferase.
Eds. van der Tweel,W.J.J., Harder,A. and Buitelaar,R.M.
Use of neural networks to predict hydration sites in proteins.
Binding of an Antiviral Agent to a Sensitive and a Resistant Human Rhinovirus.
Computer Simulations Studies with Sampling of Amino Acid Side-chain Conformations.
J. Mol. Biol. (1992) 225, 679-696.
J. Mol. Biol., (1992) 225, 697-712.
J. Am. Chem. Soc. (1992), 114, 8284-8285.
Wade,R.C., Mazor,M.H., McCammon,J.A. and Quiocho,F.A.
A Molecular Dynamics Study of Thermodynamic and Structural Aspects of the Hydration of Cavities in Proteins.
Academic Press, Inc., San Diego (1990) pp61-74.
Solvation of the Active Site of Cytochrome P450-cam.
J. Comp. Aided Mol. Des. (1990) 4, 199-204.
Hydration of Cavities in Proteins: a Molecular Dynamics Approach.
Prog. Clin. Biol. Res. (1989) 289, pp433-444.
Boobbyer,D.N.A., Goodford,P.J., McWhinnie,P.M. and Wade,R.C.
New Hydrogen-bond Potentials for Use in Determining Energetically Favourable Binding Sites on Molecules of Known Structure.
J. Mol. Graph. (1989) 7, 103-108.
Br. J. Pharmac. Proc. Suppl. (1988) 95, 588P.
D.Phil. Thesis, University of Oxford (1988).
Bachelor’s thesis, Molecular Biotechnology, Faculty of Biosciences, Ruperto-Carola University of Heidelberg, Germany (HITS).
A computational approach to decipher chromatosome structure determinants.
Ph.D. Thesis, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg, Germany (HITS).
Modeling and Simulation of Membrane Proteins to Understand their Structure, Dynamics and Function.
Development of Hydrodynamic Coarse-Grain Models for Brownian Dynamics Simulations of Crowded Protein Systems.
Master’s thesis, Physics, Ruperto-Carola University of Heidelberg, Germany (HITS).
Towards development of Random Acceleration Molecular Dynamics simulation analysis software for predicting drug residence time.
Bachelor’s thesis, Molecular Biotechnology, Faculty of Biosciences Ruprecht-Karls University, Heidelberg, Germany (HITS).
Computational Studies on the Relation Between Macromolecular Dynamics and Protein Binding and Function.
Modeling and Simulation of Protein-Surface Interactions.
Case Study of Human Growth Hormone Interactions by Brownian Dynamics Simulation.
Bachelor’s thesis, Biological Science, Faculty of Biosciences Ruprecht-Karls University, Heidelberg, Germany. (HITS).
Macromolecular Interactions: in silico prediction of the structures of complexes between proteins.
Ph.D. Thesis, Faculty of Informatics and Mathematics, Johann Wolfgang Goethe Universität, Frankfurt am Main, Germany (HITS).
Clustering and Scoring the Druggability of Transient Protein Pockets.
Bachelor’s thesis, Molecular Biotechnology, Faculty of Biosciences Ruprecht-Karls University, Heidelberg, Germany. (HITS).
Brownian Dynamics Simulations of Chymotrypsin Inhibitor 2 in Concentrated Protein Solutions.
Methods to Compute and Investigate Drug Binding Kinetics.
Master’s Thesis, Life Science Informatics, University of Bonn, Germany. (HITS).
Multiscale Simulations of Cytochrome P450 Systems.
PhD thesis, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg, Germany. (HITS).
Comparative analysis of Adenylyl Cyclase binding sites.
An Algorithmic Approach to Peptidomimetics.
Master’s thesis, Masters Programme in Life Science Informatics Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, Germany. (HITS).
Dynamische hybride Cloud für wissenschaftliche Anwendungen.
Master’s thesis, Fakultaet fuer Mathematik und Informatik Ruprecht-Karls University, Heidelberg, Germany. (HITS).
Sequence, Structure and Stability of Collagen and its Interaction with Collagenase.
PhD thesis, University of Madras, Chennai., India. (Visiting Ph. D. Student (DAAD Sandwich Scholar) to HITS from Central Leather Research Institute (CLRI)).
PhD thesis, Faculty of Chemistry, Technical University of Munich, Germany. (HITS), (TUM) .
Structural Comparison of Pyruvate Kinases.
Master’s thesis, Faculty of Biosciences, Ruprecht-Karls University Heidelberg, Germany. (HITS).
PhD thesis, Doctoral School of Science and Technologies for Health Products, University of Modena and Reggio Emilia, Italy. (Visiting Phd Student to HITS from University of Modena).
PhD thesis, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University,Heidelberg, Germany. (HITS).
Automatisierte Analyse von Brownian Dynamics Simulationen.
Master’s thesis, Bioinformatics, Giessen-Friedberg University of Applied Sciences, Germany. (HITS).
PhD thesis, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University, Heidelberg, Germany. (HITS).
Master’s thesis, Bioinformatics, University Paris VII, France. (HITS).
Diplom thesis, Physics, Ruperto-Carola University,Heidelberg, Germany. (HITS).
The Protein Structure Annotation Tool ProSAT2.
Studienarbeit, Computer Science, University of Karlsruhe, Germany . (HITS).
Master’s thesis, Bioinformatics and Modeling, National Institute of Applied Science (INSA) Lyon, France. (HITS).
Master’s thesis, Molecular Biology, Ruperto-Carola University,Heidelberg, Germany. (HITS).
Master’s thesis, Molecular Biotechnology, Uppsala University School of Engineering, Uppsala, Sweden. (HITS).
Diplom thesis, Physics, Ruperto-Carola University,Heidelberg, Germany. (EML).
Using Sequence Information in Protein Docking Procedures.
Master’s thesis, Bioinformatics, University of Applied Sciences Berlin, Germany. (EML).
Master’s thesis, Bioinformatics, Exeter University, Exeter, United Kingdom. (EMBL).
Master’s thesis, Bioinformatics, Cologne University Bioinformatics Center, University of Cologne, Germany. (EMBL).
Diplom thesis, Biology, Ruperto-Carola University,Heidelberg Germany. (EML/EMBL).
PhD thesis, University of Modena and Reggio Emilia, Modena, Italy, . (Visiting Ph.D. student to EMBL from University of Modena).
PhD thesis, Universite Joseph Fourier, Grenoble, France. (EMBL).
Computational studies of blue copper proteins.
PhD thesis, University of Modena and Reggio Emilia, Modena, Italy . (Visiting Ph.D. student to EMBL from University of Modena).
Master’s thesis, University of York, United Kingdom. (EMBL).
Diplom thesis, Biology, Eberhard-Karls University, Tubingen, Germany, . (EMBL).
Binding of Glycosaminoglycans to Heparin-Binding Proteins.
PhD thesis, University of Vienna, Austria. (Visiting Ph.D. student to EMBL from University of Vienna).
Diplom thesis, Computer Science, University of Karlsruhe, Tubingen, Germany. (EMBL).
PhD thesis, University of Alcala de Henares, Madrid, Spain. (EMBL).
PhD thesis, Ludwig-Maximilians University, Munich, Germany. (EMBL).
Diplom thesis, Biology, Ruperto-Carola University, Heidelberg, Germany. (EMBL).
Early career researchers want Open Science.
Genome Biology (2017), 18:221. (Fulltext).
PLoS Comput Biol., (2015) 11(2):e1003972. (Fulltext).
Aidan Budd, Holger Dinkel, Manuel Corpas, Jonathan C. Fuller, Laura Rubinat, Damien P. Devos, Pierre H. Khoueiry, Konrad U. Förstner, Fotis Georgatos, Francis Rowland, Malvika Sharan, Janos X. Binder, Tom Grace, Karyn Traphagen, Adam Gristwood, Natasha T. Wood.
PLoS Comput Biol., (2015) 11(1):e1003905. (Fulltext).
EMBO reports. (2013) 14:302-4. (Abstract).
Spektrum der Wissenschaft Extra (2011) 2, 14-17 (Fulltext).
“Peptides binding to the dimer interface of thymidylate synthase for the treatment of cancer” United States Patent No.: US 8,916,679 B2, Date of Patent: 23.12.2014. Filed: 17.08.2012, 01.12.2009; Costi MP, Marverti G, Cardinale D, Venturelli A, Ferrari S, Ponterini G (Univ. Modena), Henrich S, Salo-Ahen O, Wade R. (HITS).
“Uso di inhibitori della Pteridina Reduttasi per la prevenzione e/o il trattamento di infezioni parassitarie”, Italian Patent Nr. 1403584, Date of Patent: 31.10.2013, Filed : 25.11.2010; Costi MP, Luciani R, Nerini E, Guerrieri D, Ferrari S, Venturelli A, Lazzari S, (Univ. Modena); Wade R, Henrich S, Motiejunas D. (HITS).

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