Weidner P, Saar D, Söhn M, Schroeder T, Yu Y, Zöllner FG, Ponelies N, Zhou X, Zwicky A, Rohrbacher FN, Pattabiraman VR, Tanriver M, Bauer A, Ahmed H, Ametamey SM, Riffel P, Seger R, Bode JW, Wade RC, Ebert MP, Kragelund BB, Burgermeister E (2024). Myotubularin-related-protein-7 inhibits mutant (G12V) K-RAS by direct interaction, Cancer Letters 588:216783 1841
Schimunek J, Seidl P, Elez K, Hempel T, Le T, Noé F, Olsson S, Raich L, Winter R, Gokcan H, Gusev F, Gutkin EM, Isayev O, Kurnikova MG, Narangoda CH, Zubatyuk R, Bosko IP, Furs KV, Karpenko AD, Kornoushenko YV, Shuldau M, Yushkevich A, Benabderrahmane M, Bousquet-Melou P, Bureau R, Charton B, Cirou B, Gil G, Allen WJ, Sirimulla S, Watowich S, Antonopoulos N, Epitropakis N, Krasoulis A, Pitsikalis V, Theodorakis S, Kozlovskii I, Maliutin A, Medvedev A, Popov P, Zaretckii M, Eghbal-zadeh H, Halmich C, Hochreiter S, Mayr A, Ruch P, Widrich M, Berenger F, Kumar A, Yamanishi Y, Zhang K, Bengio E, Bengio Y, Jain M, Korablyov M, Liu C, Gilles M, Glaab E, Barnsley K, Iyengar SM, Ondrechen MJ, Haupt VJ, Kaiser F, Schroeder M, Pugliese L, Albani S, Athanasiou C, Beccari A, Carloni P, D’Arrigo G, Gianquinto E, Goßen J, Hanke A, Joseph BP, Kokh DB, Kovachka S, Manelfi C, Mukherjee G, Muñiz-Chicharro A, Musiani F, Nunes-Alves A, Paiardi G, Rossetti G, Sadiq SK, Spyrakis F, Talarico C, Tsengenes A, Wade R, Copeland C, Gaiser J, Olson DR, Roy A, Venkatraman V, Wheeler TJ, Arthanari H, Blaschitz K, Cespugli M, Durmaz V, Fackeldey K, Fischer PD, Gorgulla C, Gruber C, Gruber K, Hetmann M, Kinney JE, Das KMP, Pandita S, Singh A, Steinkellner G, Tesseyre G, Wagner G, Wang Z, Yust RJ, Druzhilovskiy DS, Filimonov D, Pogodin PV, Poroikov V, Rudik AV, Stolbov LA, Veselovsky AV, Rosa MD, Simone GD, Gulotta MR, Lombino J, Mekni N, Perricone U, Casini A, Embree A, Gordon DB, Lei D, Pratt K, Voigt CA, Chen K, Jacob Y, Krischuns T, Lafaye P, Zettor A, Rodríguez ML, White KM, Fearon D, Delft Fv, Walsh MA, Horvath D, Brooks CL, Falsafi B, Ford B, García-Sastre A, Lee SY, Naffakh N, Varnek A, Klambauer G, Hermans TM (2024). A community effort in SARS‐CoV‐2 drug discovery, Molecular Informatics 43(1),e202300262 1723
Perez S, Makshakova O, Angulo J, Bedini E, Bisio A, Paz JLd, Fadda E, Guerrini M, Hricovini M, Hricovini M, Lisacek F, Nieto PM, Pagel K, Pairardi G, Richter R, Samsonov SA, Vivès RA, Nikitovic D, Blum SR (2023). Glycosaminoglycans: What Remains To Be Deciphered?, JACS Au 3(3):628-656 1636
Salo-Ahen OMH, Alanko I, Bhadane R, Bonvin AMJJ, Honorato RV, Hossain S, Juffer AH, Kabedev A, Lahtela-Kakkonen M, Larsen AS, Lescrinier E, Marimuthu P, Mirza MU, Mustafa G, Nunes-Alves A, Pantsar T, Saadabadi A, Singaravelu K, Vanmeert M (2021). Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development, Processes 9(1):71 1162
Calogeropoulou T, Magoulas GE, Pöhner I, Panecka-Hofman J, Linciano P, Ferrari S, Santarem N, Jiménez-Antón MD, Olías-Molero AI, Alunda JM, Silva ACd, Wade RC, Costi MP (2019). Hits and Lead Discovery in the Identification of New Drugs against the Trypanosomatidic Infections, Medicinal Chemistry of Neglected and Tropical Diseases: Advances in the Design and Synthesis of Antimicrobial Agents, Eds Venkatesan Jayaprakash, Daniele Castagnolo, Yusuf Özkay, Chapter 10, pp 185-231, CRC Press 727
Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux J, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Pizio AD, Niv MY, Nussinov R, Tsai C, Jang H, Padhorny D, Kozakov D, McLeish T (2019). Allostery in Its Many Disguises: From Theory to Applications, Structure 27(4):566-578 549
Moraes CB, Witt G, Kuzikov M, Ellinger B, Calogeropoulou T, Prousis KC, Mangani S, Pisa FD, Landi G, Iacono LD, Pozzi C, Freitas-Junior LH, Pascoalino BdS, Bertolacini CP, Behrens B, Keminer O, Leu J, Wolf M, Reinshagen J, Cordeiro-da-Silva A, Santarem N, Venturelli A, Wrigley S, Karunakaran D, Kebede B, Pöhner I, Müller W, Panecka-Hofman J, Wade RC, Fenske M, Clos J, Alunda JM, Corral MJ, Uliassi E, Bolognesi ML, Linciano P, Quotadamo A, Ferrari S, Santucci M, Borsari C, Costi MP, Gul S (2019). Accelerating Drug Discovery Efforts for Trypanosomatidic Infections Using an Integrated Transnational Academic Drug Discovery Platform, SLAS DISCOVERY: Advancing the Science of Drug Discovery 24(3):346-361 1075
Farnham A, Kurz C, Öztürk MA, Solbiati M, Myllyntaus O, Meekes J, Pham TM, Paz C, Langiewicz M, Andrews S, Kanninen L, Agbemabiese C, Guler AT, Durieux J, Jasim S, Viessmann O, Frattini S, Yembergenova D, Benito CM, Porte M, Grangeray-Vilmint A, Curiel RP, Rehncrona C, Malas T, Esposito F, Hettne K (2017). Early career researchers want Open Science, Genome Biol 18(1),221 268
Linciano P, Dawson A, Pöhner I, Costa DM, Sá MS, Cordeiro-da-Silva A, Luciani R, Gul S, Witt G, Ellinger B, Kuzikov M, Gribbon P, Reinshagen J, Wolf M, Behrens B, Hannaert V, Michels PAM, Nerini E, Pozzi C, Pisa Fd, Landi G, Santarem N, Ferrari S, Saxena P, Lazzari S, Cannazza G, Freitas-Junior LH, Moraes CB, Pascoalino BS, Alcântara LM, Bertolacini CP, Fontana V, Wittig U, Müller W, Wade RC, Hunter WN, Mangani S, Costantino L, Costi MP (2017). Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma brucei Pteridine Reductase in Support of Early-Stage Drug Discovery, ACS Omega 2(9):5666-5683 270
Schuetz DA, Witte WEAd, Wong YC, Knasmueller B, Richter L, Kokh DB, Sadiq SK, Bosma R, Nederpelt I, Heitman LH, Segala E, Amaral M, Guo D, Andres D, Georgi V, Stoddart LA, Hill S, Cooke RM, Graaf CD, Leurs R, Frech M, Wade RC, Lange ECMd, IJzerman AP, Müller-Fahrnow A, Ecker GF (2017). Kinetics for Drug Discovery: an industry-driven effort to target drug residence time, Drug Discovery Today 22(6):896-911 276
Borsari C, Luciani R, Pozzi C, Poehner I, Henrich S, Trande M, Cordeiro-da-Silva A, Santarem N, Baptista C, Tait A, Pisa FD, Iacono LD, Landi G, Gul S, Wolf M, Kuzikov M, Ellinger B, Reinshagen J, Witt G, Gribbon P, Kohler M, Keminer O, Behrens B, Costantino L, Nevado PT, Bifeld E, Eick J, Clos J, Torrado J, Jiménez-Antón MD, Corral MJ, Alunda JM, Pellati F, Wade RC, Ferrari S, Mangani S, Costi MP (2016). Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs, J. Med. Chem. 59(16):7598-7616 174
Gdynia G, Sauer SW, Kopitz J, Fuchs D, Duglova K, Ruppert T, Miller M, Pahl J, Cerwenka A, Enders M, Mairbäurl H, Kamiński MM, Penzel R, Zhang C, Fuller JC, Wade RC, Benner A, Chang-Claude J, Brenner H, Hoffmeister M, Zentgraf H, Schirmacher P, Roth W (2016). The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration, Nat Commun 7(1),10764 735
Budd A, Dinkel H, Corpas M, Fuller JC, Rubinat L, Devos DP, Khoueiry PH, Förstner KU, Georgatos F, Rowland F, Sharan M, Binder JX, Grace T, Traphagen K, Gristwood A, Wood NT (2015). Ten Simple Rules for Organizing an Unconference, PLoS Comput Biol 11(1):e1003905 737
Cardinale D, Salo-Ahen O, Guaitoli G, Ferrari S, Venturelli A, Franchini S, Battini R, Ponterini G, Wade R, Costi M (2010). Homodimeric Enzymes as Drug Targets, Protein Engineering, Design and Selection 23(2):81-89 671
Pachov GV, Gabdoulline RR, Wade RC (2009). 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:109–128 678
Pachov G, Gabdoulline RR, Wade RC (2007). Simulation of linker histone-chromatin interactions, In From Computational Biophysics to Systems Biology 2007 (CBSB07), Hansmann, Ulrich H.E.; Meinke, Jan; Mohanty, Sandipan; Zimmermann, Olav (Eds.), John von Neumann Institute for Computing, Juelich, NIC Series 36:69-74 641
Cruciani G, Carosati E, Wade RC, Baroni M (2007). Characterization of protein-binding sites and ligands using molecular interaction fields., Comprehensive Medicinal Chemistry II, (2007) volume 4, pages 237-253 650
Winn P, Zahran M, Wade R (2007). Proceedings of the International School of Physics „Enrico Fermi“ workshop on Protein Folding and Drug Design, In Comparisons of Protein Electrostatic Potentials as a Means to Understanding Function 733
Karyakin A, Motiejunas D, Wade R, Jung C (2007). FTIR studies of the redox partner interaction in cytochrome P450: The Pdx-P450cam couple, Biochimica et Biophysica Acta. General Subjects 1770:420–431 745
Stein M, Gabdoulline R, Beßon B, Wade R (2006). Beilstein Proceedings of the 2nd Conference on ’Experimental Standard Conditions of Enzyme Characterizations (ESCEC)’ em Ruedesheim (2007) em, In The Estimation of Kinetic Parameters in Systems Biology by Comparing Molecular Interaction Fields of Enzymes, pp. 237–253, 19-23 March 746
Stein M, Gabdoulline RR, Wade RC (2006). 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, vol. 34 of NIC Series, pp. 129–132 689
K. S, T. W, R.C. W (2006). Molecular Docking, In Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, pp. pp1149–1153, Ed. Ganten,D. and Ruckpaul, K., Springer 690
Cruciani G, Carosati E, Wade R, Baroni M (2006). Characterization of Protein- Binding Sites and Ligands Using Molecular Interaction Fields, In Comprehensive Medicinal Chemistry II, vol. 4, pp. 237–253, Ed. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford 747
Motiejunas D, Wade R (2006). Structural, Energetic and Dynamic Aspects of Ligand-Receptor Interactions, In Comprehensive Medicinal Chemistry II, vol. 4, pp. pp.193–213, Ed. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford 748
Stein M, Gabdoulline R, Wade R (2006). From Computational Biophysics to Systems Biology 2006, In Integrating Structural and Kinetic Enzymatic Information in Systems Biology, vol. 34 of NIC Series, pp. 129–132, Hansmann, Ulrich H.E.; Meinke, Jan; Mohanty, Sandipan; Zimmermann, Olav (Eds.) 749
Wang T, Wade R (2006). Force Field Effects on a b-sheet Protein Domain Structure in Thermal Unfolding Simulations, J Chem Theory and Comput 2:140–148 750
Wade RC (2005). Calculation and Application of Molecular Interaction Fields, In Molecular Interaction Fields. Applications in Drug Discovery and ADME Prediction, pp. Ch. 2, pp27–42, Ed. Cruciani, G., Wiley-VCH, Weinheim, ISBN 3-527-31087-8 697
Damborsky J, Kmunicek J, Jedlicka T, Luengo S, Gago F, Ortiz AR, Wade RC (2004). Rational Re-design of Haloalkane Dehalogenases Guided by Comparative Binding Energy Analysis, In Enzyme functionality: Design, Engineering and Screening, pp. pp79–96, Ed. A. Svendsen, Marcel Dekker, New York 710
Essigke T, Ullmann GM, Wade RC (2003). What Determines the Redox Potential of Ferredoxins?, In „Proceedings of the 13th International Conference on Cytochromes P450“, pp. 25–30, Monduzzi Editore, Bologna 714
Essigke T, Ullmann M, Wade R (2003). Proceedings of the 13textsuperscriptth International Conference on Cytochromes P450, In What Determines the Redox Potential of Ferredoxins?, pp. pp25–30, Monduzzi Editore, Bologna 752
Rienzo FD, Gabdoulline RR, Wade RC, Menziani MC (2002). Biologically relevant properties of copper-containing proteins analysed by means of semi-quantitative and quantitative theoretical descriptors, In Handbook of Copper Pharmacology and Toxicology, pp. pp. 53–80, Ed. E. J. Massaro, Humana Press, Totowa, New Jersey 726
Wang T, Wade R (2001). COMBINE 3D-QSAR analysis of Influenza Neuraminidase Inhibitors, In Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships, pp. pp78–82, Eds. Holtje, H-D., Sippl,W., Prous Science S.A., Barcelona 762
Helms V, Wade R (1997). Free energies of hydration from thermodynamic integration: A comparison of molecular mechanics force fields and evaluation of calculations accuracy, J. Comp. Chem. 18:449–462 806
Wade R, Lounnas V, Helms V, Hoa GHB, Primo CD, Deprez E, Barret C, Kozin S, Jung C, Schulze H, Contzen J, Mouro C, Gill E, Simonneaux G, Bondon A, LeGrand N, Schlichting I (1996). Fundamentals of Enzyme-Ligand Interactions in Cytochrome P450cam, p. 3, Ed. M.J. Geisow, BIODIGM, Nottingham 811
Ortiz A, Pisabarro M, Gago F, Wade R (1995). Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis: Application to Human Synovial Fluid Phospholipase A2 Inhibitors, In QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications, pp. pp439–443, Eds. Sanz,F., Giraldo,J., Manaut,F, J.R. Prous Science Publishers, Barcelona 818
Wade R (1993). Molecular Interaction Fields, In 3D QSAR in Drug Design. Theory, Methods and Applications, pp. pp486–505, Ed. Kubinyi,H. ESCOM, Leiden 838
Wade R (1990). An Approach to the Design of Anti-Influenza Agents, In Use of X-Ray Crystallography in the Design of Antiviral Agents, pp. pp61–74, Eds. Laver,G. and Air,G. Academic Press, Inc., San Diego 843
Structural bioinformatics approach to exploring transient binding pockets in proteins (Bachelor’s Thesis), Faculty of Biosciences and Faculty of Chemistry and Earth Sciences, Ruprecht-Karls University, Heidelberg 1899
Structural bioinformatics approach to exploring transient binding pockets in proteins, (Bachelor’s Thesis), Biochemistry, Faculty of Biosciences and Faculty of Chemistry and Earth Sciences, Ruprecht-Karls University, Heidelberg (Bachelor’s Thesis)1874
Investigation of the impact of mutations in Cytochrome P450 reductase on the rate of electron transfer to Cytochrome P450 by molecular dynamics simulations (Master’s Thesis), Chemistry, Department of Chemistry, Ruprecht-Karls University, Heidelberg 1898
2023
Nießner J (2023). Computational Models of Hen Egg White Lysozyme Physisorption to Silica- and Mica-like Surfaces (Master’s Thesis), Physics, Department of Physics and Astronomy, Ruprecht-Karls University, Heidelberg 1759
Athanasiou C (2023). Modeling of mechanistic effects of neurotrophin modulators (Doctoral Thesis), Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1760
Tarnow M (2023). Optimization of a Drug: Polymer Formulation Exploiting a Computational Approach based on Molecular Dynamics Simulations (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Engineering Sciences, Ruprecht-Karls University, Heidelberg 1762
Ferraz M (2023). Enhanced sampling simulations and machine learning to address infectious diseases (Doctoral Thesis), Chemistry, Department of Chemistry, Federal University of Pernambuco, Recife, Brazil 1785
2022
Kaeser M (2022). Computational Investigation of the Structure Kinetics Relationship of Small-Molecule Compounds Binding the Histamine-1-Receptor (Master’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1582
Teuffel J (2022). Molecular Dynamics Simulation of a Mammalian Cytochrome P450 Protein and its Interaction with Substrates and Redox-Partners (Master’s Thesis), Biochemistry, Faculty of Biosciences and Faculty of Chemistry and Earth Sciences, Ruprecht-Karls University, Heidelberg 1445
Emmert M (2022). Generation and Testing of Boltzmann Generators Trained on Peptide Molecular Dynamics Simulations to Predict Peptide Conformational Behaviour (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1579
Hanke A (2022). P. falciparum Circumsporozoite protein epitope/paratope interactions: Addressing the key role of molecular flexibility (Master’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1580
Cabezudo AC (2022). Structural Insights into Neurotrophin Receptor Dimerization using Coarse-grained Molecular Dynamics Simulations (Master’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1581
2021
Dohrke J (2021). Molecular mechanisms of AMPAR modulation by auxiliary subunits (Master’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1207
Marinis PD (2021). Assessing ML-database augmentation approaches
for Druggability Score calculations in TRAPP-pocket (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1441
Messner L (2021). Comparison of ligand docking to the AMPAR-TARP interaction site between different isoforms (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg, 2021 1442
Han SB (2021). Multi-Resolution Simulation Study of CYP 2B4 to Investigate Complex Formation with Human NADPH-Cytochrome P450 Oxidoreductase in Lipid Bilayer (Master’s Thesis), Molecular Biosciences, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1443
Ormersbach F (2020). Computational ligand superimposition and analysis of protein-ligand interaction fingerprints (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1204
Jarosch L (2020). Computational modeling of SERCA interactions with S100A1ct and DWORF fingerprints (Bachelor’s Thesis), Biochemistry, Faculty of Biosciences and Faculty of Chemistry and Geosciences, Ruprecht-Karls University, Heidelberg 1205
Hanke A (2019). Computational characterisation of protein homo- and heterodimer formation (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1010
Ullmann P (2019). Molecular dynamics simulation studies of gp41 cytoplasmic tail lateral embedding in phospholipid bilayer (Bachelor’s Thesis), Biosciences, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1011
Yuan J (2019). Druggability Assessment in TRAPP Procedure using Machine Learning Approaches (Master’s Thesis), Master of Scientific Computing, Fakultät für Mathematik und Informatik, Ruprecht-Karls University, Heidelberg 1012
Ganotra GK (2019). Computational studies of drug-binding kinetics (Doctoral Thesis), Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University, Heidelberg 1013
2018
Friedrich P (2018). A novel method to treat gated protein-ligand binding via on-the-fly conformational updates within rigid body BD simulations (Master’s Thesis), Faculty of Physics, Ruprecht-Karls University Heidelberg 880
Öztuerk MA (2018). A computational approach to decipher chromatosome structure determinants (Doctoral Thesis), Combined Faculties of the Natural Sciences and for Mathematics, Ruprecht-Karls University Heidelberg 882
Dohrke J (2018). Modelling of Neurotrophin Receptors (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg 1032
2017
Reinhardt M (2017). Development of Hydrodynamic Coarse-Grain Models for Brownian Dynamics Simulations of Crowded Protein Systems (Master’s Thesis), Faculty of Physics, Ruprecht-Karls University Heidelberg 877
Mustafa G (2017). Modeling and Simulation of Membrane Proteins to Understand their Structure, Dynamics and Function (Doctoral Thesis), Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg 878
Buerkel C (2017). 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 1031
2016
Ozboyaci M (2016). Modeling and Simulation of Protein-Surface Interactions (Doctoral Thesis), Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg 876
Stubbusch A (2016). Case Study of Human Growth Hormone Interactions by Brownian Dynamics Simulation (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg 1030
2015
Berinski M (2015). Macromolecular Interactions: in silico prediction of the structures of complexes between proteins (Doctoral Thesis), Faculty of Informatics and Mathematics, Johann Wolfgang Goethe Universität, Frankfurt am Main 883
Ganotra GK (2015). Methods to Compute and Investigate Drug Binding Kinetics (Master’s Thesis), Life Science Informatics, University of Bonn 884
Yu X (2015). Multiscale Simulations of Cytochrome P450 Systems (Doctoral Thesis), Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg 885
Horn M (2015). Clustering and Scoring the Druggability of Transient Protein Pockets (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg 1028
Waldhauer M (2015). Brownian Dynamics Simulations of Chymotrypsin Inhibitor 2 in Concentrated Protein Solutions (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg 1029
2014
Tong R (2014). Comparative analysis of Adenylyl Cyclase binding sites (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1027
2013
Banerjee P (2013). 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 852
2012
Monninger T (2012). Dynamische hybride Cloud für wissenschaftliche Anwendungen (Master’s Thesis), Fakultaet fuer Mathematik und Informatik, Ruprecht-Karls University, Heidelberg 853
2011
Subramaniam SR (2011). Sequence, Structure and Stability of Collagen and its Interaction with Collagenase. (Doctoral Thesis), University of Madras, Chennai. 854
Garg D (2011). Computational and NMR Studies of Thymidylate Synthase and its Regulation (Doctoral Thesis), Faculty of Chemistry, Technical University of Munich 855
Veith N (2011). Structural Comparison of Pyruvate Kinases. (Master’s Thesis), Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 856
Nerini E (2011). System Approach to the Identification of Folate-related Enzyme Inhibitors with Anti-infectious Action (Doctoral Thesis), Doctoral School of Science and Technologies for Health Products, University of Modena and Reggio Emilia 857
2010
Feldman-Salit A (2010). Computation and Modeling of Molecular Recognition: The Cysteine Synthase Complex (Doctoral Thesis), Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg 858
2009
Pachov GV (2009). Linker Histone-Nucleosome Interactions: A Modelling and Simulation Study (Doctoral Thesis), Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University,Heidelberg 859
Berynskyy M (2009). Automatisierte Analyse von Brownian Dynamics Simulationen (Master’s Thesis), Bioinformatics, Giessen-Friedberg University of Applied Sciences 860
2007
Motiejunas D (2007). Modeling of macromolecular interactions (Doctoral Thesis), Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University, Heidelberg 861
2006
Zahran M (2006). Analyse a haut debit des proprietes electrostatiques des proteines de la famille des ubiquitines (High-throughput analysis of the electrostatic properties of proteins of the ubiquitin family) (Master’s Thesis), Bioinformatics, University Paris VII 862
2005
Besson B (2005). Development of a software to aid the search of protein structural information to estimate kinetic parameters in systems biology applications (Master’s Thesis), Bioinformatics and Modeling, National Institute of Applied Science (INSA) Lyon 863
Johann TI (2005). Perturbation Methods in Molecular Dynamics Simulations with Implicit Solvent Models (Diplom Thesis), Physics, Ruperto-Carola University, Heidelberg 1014
2004
Motiejunas D (2004). Protein-protein docking assisted by sequence conservation and experimental data (Master’s Thesis), Molecular Biology, Ruperto-Carola University,Heidelberg 864
R.Hallingbaeck H (2004). Peroxidases: A computational study of ligand binding and enzyme kinetics (Master’s Thesis), Molecular Biotechnology, Uppsala University School of Engineering, Uppsala 865
2003
Doudieu OMN (2003). Using Sequence Information in Protein Docking Procedures (Master’s Thesis), Bioinformatics, University of Applied Sciences, Berlin 866
Battey JN (2003). High-throughput Structural and Electrostatic Modelling of Ubiquitin Conjugating Enzymes (Master’s Thesis), Bioinformatics, Exeter University, Exeter 867
Pulagam LVP (2003). Structure-based design of inhibitors of enzymes of the ubiquitin mediated protein degradation pathway (Master’s Thesis), Bioinformatics, Cologne University Bioinformatics Center, University of Cologne 868
Neumann GF (2003). Entwicklung einer erweiterten Anwendung der Hauptkomponentenanalyse fuer das Protein-Protein Dockingproblem (Diplom Thesis), Physics, Ruperto-Carola University, Heidelberg 1015
2001
Ferrari S (2001). Inhibition studies of enzymes involved in drug resistance phenomena. Library-design and Structure-based approaches towards species-specific inhibitors of Thymidylate Synthase (Doctoral Thesis), University of Modena and Reggio Emilia, Modena 869
Nardi F (1999). Molecular Dynamics and NMR Spectroscopic Studies of Local Interactions of Small Peptides in Aqueous Solution Involving Aromatic Residues (Doctoral Thesis), Universite Joseph Fourier, Grenoble 870
Rienzo FD (1999). Computational studies of blue copper proteins (Doctoral Thesis), University of Modena and Reggio Emilia, Modena 871
Koboyashi M (1999). Chloride ion exchange routes in Haloalkane Dehalogenase from Xanthobacter autrophicus detected by Thermal Motion Pathway analysis, GRID and Essential Dynamics (Master’s Thesis), University of York 872
Gauges R (1999). Molekulardynamische Simulation zur Aufklaerung des Substratzuganges in Cytochrom P450eryF (Diplom Thesis), Biology, Eberhard-Karls University, Tubingen 1017
1998
Bitomsky W (1998). Binding of Glycosaminoglycans to Heparin-Binding Proteins (Doctoral Thesis), University of Vienna 873
1996
Ortiz AR (1996). Rational design of Human Synovial Fluid Phospholipase A2 inhibitors and analysis of their three-dimensional structure-activity relationships (Doctoral Thesis), University of Alcala de Henares, Madrid 874
Helms V (1996). Hydratation des aktiven Zentrums von Cytochrom P450cam – Untersuchung mit Molekueldynamik-Simulationen (Doctoral Thesis), Ludwig-Maximilians University, Munich 875
Reimer N (1996). Dynamische Einstellung des Parallelitaetsgrades mit reflexiven Programmen (Diplom Thesis), Computer Science, University of Karlsruhe, Tubingen 1018
1995
Degenhardt M (1995). De-Novo Design von Liganden zur Blockierung der Substratzugaenlichkeit von Cytochrom P450cam (Diplom Thesis), Biology, Ruperto-Carola University, Heidelberg 1019
1988
Wade R (1988). Ligand-Macromolecule Interactions (Doctoral Thesis), University of Oxford 850
2013
Costi MP, Luciani R, Nerini E, D. G, Ferrari S, Venturelli A, Lazzari S, Wade RC, Henrich S, Motiejunas D (2013). 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 1034
2009
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