This picture showsJürgen Pleiss

Apl. Prof. Dr.

Jürgen Pleiss

Bioinformatics Group Leader
Institute of Biochemistry and Technical Biochemistry
Technical Biochemistry


+49 711 685-63191

Allmandring 31
70569 Stuttgart
Room: 0.307

  1. 2020

    1. Lohoff, C., Buchholz, P., Le, R.-H. M., & Pleiss, J. (2020). The Expansin Engineering Database: a navigation and classification tool for expansins and homologues. Proteins, 89, 149–162.
    2. Bauer, T., Buchholz, P., & Pleiss, J. (2020). The modular structure of α/β-hydrolases. FEBS J, 287, 1035–1053.
    3. Mangiagalli, M., Carvalho, H., Natalello, A., Ferrario, V., Pennati, M., Barbiroli, A., Lotti, M., Pleiss, J., & Brocca, S. (2020). Diverse effects of aqueous polar co-solvents on Candida antarctica lipase B. Int J Biol Macromol, 150, 930–940.
    4. Gygli, G., Xu, X., & Pleiss, J. (2020). Meta-analysis of viscosity of aqueous deep eutectic solvents and their components. Sci Rep, 10, 21395–21395.
    5. Gräff, M., Buchholz, P., Le Roes-Hill, M., & Pleiss, J. (2020). Multicopper oxidases: modular structure, sequence space and evolutionary relationships. Proteins.
    6. Roth, S., Stockinger, P., Steff, J., Steimle, S., Sautner, V., Tittmann, K., Pleiss, J., & Müller, M. (2020). Crossing the border: From keto- to imine reduction in short-chain dehydrogenases/reductases. ChemBioChem, 21, 2615–2619.
    7. Stockinger, P., Schelle, L., Schober, B., Buchholz, P., Pleiss, J., & Nestl, B. (2020). Engineering of thermostable β-hydroxyacid dehydrogenase for asymmetric reduction of imines. ChemBioChem, 21, 3511–3514.
    8. Eisenkolb, I., Jensch, A., Eisenkolb, K., Kramer, A., Buchholz, P., Pleiss, J., Spiess, A., & Radde, N. (2020). Modeling of biocatalytic reactions: A workflow for model calibration, selection and validation using Bayesian statistics. AIChE J, 66, e16866.
    9. Gygli, G., & Pleiss, J. (2020). Simulation Foundry: automated and F.A.I.R. molecular modelling. J Chem Inf Model, 60, 1922–1927.
    10. Malzacher, S., Range, J., Halupczok, C., Pleiss, J., & Rother, D. (2020). BioCatHub, a graphical user interface for standardized data acquisition in biocatalysis. Chem Ing Tech, 92, 1251–1251.
    11. Rifai, E., Ferrario, V., Pleiss, J., & Geerke, D. (2020). A combined linear interaction energy and alchemical solvation free energy approach for protein-binding anity computation. J Chem Theory Comput, 16, 1300–1310.
    12. Stockinger, P., Roth, S., Müller, M., & Pleiss, J. (2020). Systematic evaluation of imine-reducing enzymes: Common principles in imine reductases, β-hydroxyacid dehydrogenases, and short-chain dehydrogenases/reductases. ChemBioChem, 21, 2689–2695.
    13. Xu, X., Range, J., Gygli, G., & Pleiss, J. (2020). Analysis of thermophysical properties of deep eutectic solvents by data integration. J Chem Eng Data, 65, 1172–1179.
  2. 2019

    1. Buchholz, P., Ohs, R., Spieß, A., & Pleiss, J. (2019). Progress curve analysis within BioCatNet: comparing kinetic models for enzyme-catalyzed self-ligation. Biotechnol J, 14, e1800183.
    2. Grüninger, M., Buchholz, P., Mordhorst, S., Strack, P., Müller, M., Hubrich, F., Pleiss, J., & Andexer, J. (2019). Chorismatases – the family is growing. Org Biomol Chem, 17, 2092–2098.
    3. Gobeil, S., Ebert, M., Park, J., Gagné, D., Doucet, N., Berghuis, A., Pleiss, J., & Pelletier, J. (2019). The structural dynamics of engineered β-lactamases vary broadly on three timescales yet sustain native function. Sci Rep, 9, 6656–6656.
    4. Fries, A., Mazzaferro, L., Grüning, B., Bisel, P., Stibal, K., Buchholz, P., Pleiss, J., Sprenger, G., & Müller, M. (2019). Alteration of the route to menaquinone towards isochorismate - derived metabolites. ChemBioChem, 20, 1672–1677.
    5. Baz, J., Held, C., Pleiss, J., & Hansen, N. (2019). Thermophysical properties of glyceline-water mixtures investigated by molecular modelling. Phys Chem Chem Phys, 21, 6467–6476.
    6. Buchholz, P., Ferrario, V., Pohl, M., Gardossi, L., & Pleiss, J. (2019). Navigating within thiamine diphosphate-dependent decarboxylases: Sequences, structures, functional positions, and binding sites. Proteins, 87, 774–785.
    7. Schatz, K., Krone, M., Pleiss, J., & Ertl, T. (2019). Interactive visualization of biomolecules’ dynamic and complex properties. Eur Phys J Special Topics, 227, 1725–1739.
    8. Gräff, M., Buchholz, P., Stockinger, P., Bommarius, B., Bommarius, A., & Pleiss, J. (2019). The Short-chain Dehydrogenase/Reductase Engineering Database (SDRED):  A classification and analysis system for a highly diverse enzyme family. Proteins, 87, 443–451.
    9. Demming, R., Hammer, S., Nestl, B., Gergel, S., Fademrecht, S., Pleiss, J., & Hauer, B. (2019). Asymmetric Enzymatic Hydration of Unactivated, Aliphatic Alkenes. Angew Chem Int Ed Engl, 58, 173–177.
    10. Ferrario, V., Fischer, M., Zhu, Y., & Pleiss, J. (2019). Modelling of substrate access and substrate binding to cephalosporin acylases. Sci Rep, 9, 12402.
    11. Ferrario, V., & Pleiss, J. (2019). Molecular simulations of enzymes under non-natural conditions. Eur Phys J  Special Topics, 227, 1631–1638.
    12. Roddan, R., Gygli, G., Sula, A., Mendez-Sanchez, D., Pleiss, J., Ward, J., Keep, N., & Hailes, H. (2019). The acceptance and kinetic resolution of alpha-methyl substituted aldehydes by norcoclaurine synthases. ACS Catal, 9, 9640–9649.
  3. 2018

    1. Pleiss, J. (2018). Thermodynamic activity-based progress curve analysis in enzyme kinetics. Trends Biotechnol, 36, 234–238.
    2. Baierl, A., Theorell, A., Mackfeld, U., Marquardt, P., Hoffmann, F., Moers, S., Nöh, K., Buchholz, P., Pleiss, J., & Pohl, M. (2018). Towards a mechanistic understanding of factors controlling the stereoselectivity of transketolase. ChemCatChem, 10, 2601–2611.
    3. Martínez-Martínez, M., Coscolín, C., Santiago, G., Chow, J., Stogios, P., ..., Buchholz, P., Pleiss, J., ..., & Ferrer, M. (2018). Determinants and prediction of esterase substrate promiscuity patterns. ACS Chem Biol, 13, 225–234.
    4. Lenz, M., Fademrecht, S., Sharma, M., Pleiss, J., Grogan, G., & Nestl, B. (2018). New imine-reducing enzymes from beta-hydroxyacid dehydrogenases by single amino acid substitutions. Protein Engineering, Design and Selection, 31, 109–120.
    5. Buß, O., Buchholz, P., Gräff, M., Klausmann, P., Rudat, J., & Pleiss, J. (2018). The omega-Transaminase Engineering Database (oTAED): a navigation tool in protein sequence and structure space. Proteins, 86, 566–580.
    6. Lotti, M., Pleiss, J., Valero, F., & Ferrer, P. (2018). Enzymatic production of biodiesel: strategies to overcome methanol inactivation. Biotechnol J, 13, e1700155.
    7. Ferrario, V., Hansen, N., & Pleiss, J. (2018). Interpretation of cytochrome P450 monooxygenase kinetics by modeling of thermodynamic activity. J Inorg Biochem, 183, 172–178.
    8. Ferrario, V., & Pleiss, J. (2018). Simulation of protein diffusion: a sensitive probe of protein-solvent interactions. J Biomol Struct Dyn, 37, 1534–1544.
    9. Buchholz, P., Zeil, C., & Pleiss, J. (2018). The scale-free nature of protein sequence space. PLoS One, 13, e0200815.
  4. 2017

    1. Pleiss, J. (2017). Thermodynamic activity–based interpretation of enzyme kinetics. Trends Biotechnol, 35, 379–382.
    2. Benson, S., & Pleiss, J. (2017). Self-assembly nanostructures of triglyceride-water interfaces determine functional conformations of Candida antarctica lipase B. Langmuir, 33, 3151–3159.
    3. Schmid, J., Steiner, L., Fademrecht, S., Pleiss, J., Otte, K., & Hauer, B. (2017). Biocatalytic study of novel oleate hydratases. J Mol Catal B: Enzym, 133, S243–S249.
    4. Zhang, Q., Catti, L., Pleiss, J., & Tiefenbacher, K. (2017). Terpene cyclizations inside a supramolecular catalyst: Leaving-group-controlled product selectivity and mechanistic studies. J Am Chem Soc, 139, 11482–11492.
    5. Krone, M., Friess, F., Scharnowski, K., Reina, G., Fademrecht, S., Kulschewski, T., Pleiss, J., & Ertl, T. (2017). Molecular Surface Maps. IEEE Trans Vis Comput Graph, 23, 701–710.
    6. Buchholz, P., Fademrecht, S., & Pleiss, J. (2017). Percolation in protein sequence space. PLoS One, 12, e0189646.
  5. 2016

    1. Gricman, L., Weissenborn, M., Hoffmann, S., Borlinghaus, N., Hauer, B., & Pleiss, J. (2016). Redox Partner Interaction Sites in Cytochrome P450 Monooxygenases: In Silico Analysis and Experimental Validation. ChemistrySelect, 6, 1243–1251.
    2. Kulschewski, T., & Pleiss, J. (2016). Binding of solvent molecules to a protein surface in binary mixtures follows a competitive Langmuir model. Langmuir, 32, 8960–8968.
    3. Schäfer, I., Lasko, G., Do, T., Pleiss, J., Weber, U., & Schmauder, S. (2016). Peptide–zinc oxide interaction: Finite element simulation using cohesive zone models based on molecular dynamics simulation. In S. I. Schmauder S (Ed.), Multiscale Materials Modeling. De Gruyter.
    4. Bock, S., Buchholz, P., Vogel, C., Holzapfel, A., Pleiss, J., Wiechert, W., Pohl, M., & Rother, D. (2016). Exploring the Sequence-Function Space of ThDP-Dependent Enzymes. Chemie Ingenieur Technik, 88, 1246.
    5. Pleiss, J., & Zeil, C. (2016). Reply to The Curious Case of TEM-116. Antimicrob Agents Chemother, 60, 7001–7001.
    6. Fademrecht, S., Scheller, P., Nestl, B., Hauer, B., & Pleiss, J. (2016). Identification of imine reductase-specific sequence motifs. Proteins, 84, 600–610.
    7. Widmann, M., & Pleiss, J. (2016). Sequence, structure, function: what we learn from analyzing protein families. In S. A (Ed.), Understanding enzymes. pan Standord Publishing.
    8. Hoffmann, S., Weissenborn, M., Gricman, L., Notonier, S., Pleiss, J., & Hauer, B. (2016). The Impact of Linker Length on P450 Fusion Constructs: Activity, Stability and Coupling. ChemCatChem, 8, 1591–1597.
    9. Buchholz, P., Vogel, C., Reusch, W., Pohl, M., Rother, D., Spieß, A., & Pleiss, J. (2016). BioCatNet: a database system for the integration of enzyme sequences and biocatalytic experiments. ChemBioChem, 17, 2093–2098.
    10. Eichler, A., Gricman, L., Herter, S., Kelly, P., Turner, N., Pleiss, J., & Flitsch, S. (2016). Enantioselective benzylic hydroxylation catalysed by P450 monooxygenases: characterisation of a P450cam mutant library and molecular modelling. ChemBioChem, 17, 426–432.
    11. Benson, S., & Pleiss, J. (2016). Computational modeling of a biocatalyst at a hydrophobic substrate interface. In R. M. Nagel WE Kröner DH (Ed.), High Performance Computing in Science and Engineering ´15. Springer International Publishing.
    12. Notonier, S., Gricman, L., Pleiss, J., & Hauer, B. (2016). Semi-rational protein engineering of CYP153A BM3 for efficient terminal hydroxylation of short to long chain fatty acids. ChemBioChem, 17, 1550–1557.
    13. Jozwik, I., Kiss, F., Gricman, L., Abdulmughni, A., Brill, E., Zapp, J., Pleiss, J., Bernhardt, R., & Thunnissen, A. (2016). Structural basis of steroid binding and oxidation by the cytochrome P450 CYP109E1 from Bacillus megaterium. FEBS J, 283, 4128–4148.
    14. Zeil, C., Widmann, M., Fademrecht, S., Vogel, C., & Pleiss, J. (2016). Microdiversity of TEM β-lactamases: a network analysis of sequence-function relationships and exploration of sequence space. Antimicrob Agents Chemother, 60, 2709–2717.
  6. 2015

    1. Taudt, A., Arnold, A., & Pleiss, J. (2015). Simulation of protein association - Kinetic pathways towards crystal contacts. Phys Rev E, 91, 033311.
    2. Gricman, L., Vogel, C., & Pleiss, J. (2015). Identification of universal selectivity-determining positions in cytochrome P450 monooxygenases by systematic sequence-based literature mining. Proteins, 83, 1593-1603.
    3. Sasso, F., Kulschewski, T., Secundo, F., Lotti, M., & Pleiss, J. (2015). The effect of thermodynamic properties of solvent mixtures explains the difference between methanol and ethanol in C.antarctica lipase B catalyzed alcoholysis. J Biotechnol, 214, 1–8.
    4. Prins, A., Kleinsmidt, L., Khan, N., Kirby, B., Kudanga, T., Vollmer, J., Pleiss, J., Burton, S., & Le, R.-H. M. (2015). The effect of mutations near the T1 copper site on the biochemical characteristics of the small laccase from Streptomyces coelicolor A3(2). Enzyme Microb Technol, 68, 23–32.
    5. Lotti, M., Pleiss, J., Valero, F., & Ferrer, P. (2015). Effects of methanol on lipases: molecular, kinetic and process issues in the production of biodiesel. Biotechnol J, 10, 22–30.
  7. 2014

    1. Westphal, R., Vogel, C., Schmitz, C., Pleiss, J., Müller, M., Pohl, M., & Rother, D. (2014). A Tailor-Made Chimeric Thiamine Diphosphate Dependent Enzyme for the Direct Asymmetric Synthesis of (S)-Benzoins. Angew. Chem. Int. Ed., 53, 9376–9379.
    2. Schäfer, I., Lasko, G., Do, T., Pleiss, J., Weber, U., & Schmauder, S. (2014). Peptide - zinc oxide interaction: finite element simulation using cohesive zone models based on molecular dynamics simulation. Comp Mater Sci, 95, 320–327.
    3. Westphal, R., Jansen, S., Vogel, C., Pleiss, J., Müller, M., Rother, D., & Pohl, M. (2014). MenD from Bacillus subtilis: A Potent Catalyst for the Enantiocomplementary Asymmetric Synthesis of Functionalized α-Hydroxy Ketones. ChemCatChem, 6, 1082–1088.
    4. Widmann, M., & Pleiss, J. (2014). Protein variants form a system of networks: microdiversity of IMP metallo-beta-lactamases. PLoS ONE, 9, e101813.
    5. Baier, J., Blumenstein, N., Preusker, J., Jeurgens, L., Welzel, U., Do, T., Pleiss, J., & Bill, J. (2014). The influence of ZnO-binding 12-mer peptides on bio-inspired ZnO formation. Cryst Eng Comm, 16, 5301–5307.
    6. Scharnowski, K., Krone, M., Reina, G., Kulschewski, T., Pleiss, J., & Ertl, T. (2014). Comparative Visualization of Molecular Surfaces Using Deformable Models. Comput Graph Forum, 3, 191–200.
    7. Benson, S., & Pleiss, J. (2014). Molecular dynamics simulations of self-emulsifying drug delivery systems (SEDDS): influence of excipients on droplet nanostructure and drug localization. Langmuir, 30, 8471–8480.
    8. Pleiss, J. (2014). Systematic analysis of large enzyme families: identification of specificity- and selectivity-determining hotspots. ChemCatChem, 6, 944–950.
    9. Vogel, C., & Pleiss, J. (2014). The modular structure of ThDP-dependent enzymes. Proteins, 82, 2523–2537.
    10. Bogazkaya, A., von, B. C., Kriening, S., Busch, A., Seifert, A., Pleiss, J., Laschat, S., & Urlacher, V. (2014). Selective allylic hydroxylation of acyclic terpenoids by CYP154E1 from Thermobifida fusca YX. Beilstein J. Org. Chem, 10, 1347–1353.
    11. Gricman, L., Vogel, C., & Pleiss, J. (2014). Conservation analysis of class-specific positions in cytochrome P450 monooxygenases: functional and structural relevance. Proteins, 82, 491–504.
    12. Benson, S., & Pleiss, J. (2014). Solvent Flux Method (SFM): A case study of water access to Candida antarctica lipase B. J Chem Theory Comput, 10, 5206–5214.
    13. Scheller, P., Fademrecht, S., Hofelzer, S., Pleiss, J., Leipold, F., Turner, N., Nestl, B., & Hauer, B. (2014). Enzyme Toolbox: Novel Enantiocomplementary Imine Reductases. ChemBioChem, 15, 2201–2204.
  8. 2013

    1. Kulschewski, T., Sasso, F., Secundo, F., Lotti, M., & Pleiss, J. (2013). Molecular mechanism of deactivation of C. antarctica lipase B by methanol. J Biotechnol, 168, 462–469.
    2. Krone, M., Reina, G., Schulz, C., Kulschewski, T., Pleiss, J., & Ertl, T. (2013). Interactive Extraction and Tracking of Biomolecular Surface Features. Comput Graph Forum, 32, 331–340.
    3. Benson, S., & Pleiss, J. (2013). Incomplete mixing versus clathrate-like structures: a molecular view on hydrophobicity in methanol-water mixtures. J Mol Model, 19, 3427–3436.
    4. Hailes, H., Rother, D., Müller, M., Westphal, R., Ward, J., Pleiss, J., Vogel, C., & Pohl, M. (2013). Engineering stereoselectivity of ThDP-dependent enzymes. FEBS J, 280, 6374–6394.
    5. Kulschewski, T., & Pleiss, J. (2013). A molecular dynamics study of liquid aliphatic alcohols: simulation of density and self-diffusion coefficient using a modified OPLS force field. Mol Simulat, 39, 754–767.
    6. Roduner, E., Kaim, W., Sarkar, B., Urlacher, V., Pleiss, J., Gläser, R., Einicke, W., Sprenger, G., & Beifuss, U. (2013). Selective catalytic oxidation of C–H bonds with molecular oxygen. ChemCatChem, 5, 82–112.
    7. Westphal, R., Waltzer, S., Mackfeld, U., Widmann, M., Pleiss, J., Beigi, M., Müller, M., Rother, D., & Pohl, M. (2013). (S)-Selective MenD variants from Escherichia coli provide access to new functionalized chiral 2-hydroxy ketones. Chem Commun, 49, 2061–2063.
    8. Westphal, R., Hahn, D., Mackfeld, U., Waltzer, S., Beigi, M., Widmann, M., Vogel, C., Pleiss, J., Müller, M., & Pohl, M. (2013). Tailoring (S)-selectivity of MenD from Escherichia coli. ChemCatChem, 13, 3587–3594.
  9. 2012

    1. Widmann, M., Pleiss, J., & Samland, A. (2012). Computational tools for rational protein engineering of aldolases. Comput Struct Biotechnol J, 2, e201209016–e201209016.
    2. Siedenburg, G., Jendrossek, D., Breuer, M., Juhl, B., Pleiss, J., Seitz, M., Klebensberger, J., & Hauer, B. (2012). Activation-independent cyclization of monoterpenoids. Appl Environ Microbiol, 78, 1055–1062.
    3. Gruber, C., & Pleiss, J. (2012). Molecular modeling of lipase binding to a substrate-water interface. Methods Mol Biol, 861, 313–327.
    4. Ferrario, V., Braiuca, P., Tessaro, P., Knapic, L., Gruber, C., Pleiss, J., Ebert, C., Eichhorn, E., & Gardossi, L. (2012). Elucidating the structural and conformational factors responsible for the activity and substrate specificity of alkanesulfonate monooxygenase. J Biomol Struct Dyn, 30, 74–88.
    5. Gruber, C., & Pleiss, J. (2012). Lipase B from Candida antarctica binds to hydrophobic substrate-water interfaces via hydrophobic anchors surrounding the active site entrance. J Mol Catal B, 84, 48–54.
    6. Kulschewski, T., & Pleiss, J. (2012). Simulation of enzymes in organic solvents. In S. Lutz & U. Bornscheuer (Eds.), Protein engineering handbook, vol.3. Wiley-VCH.
    7. Vogel, C., Widmann, M., Pohl, M., & Pleiss, J. (2012). A standard numbering scheme for thiamine diphosphate-dependent decarboxylases. BMC Biochemistry, 13, 24–24.
    8. Pickel, B., Pfannstiel, J., Steudle, A., Lehmann, A., Gerken, U., Pleiss, J., & Schaller, A. (2012). A model of dirigent proteins derived from structural and functional similarities with alleneoxide cyclase and lipocalins. FEBS J, 279, 1980–1993.
    9. Fademrecht, S., Juhl, P., Sirim, D., & Pleiss, J. (2012). The triterpene cyclase protein family: a systematic analysis. Proteins, 80, 2009–2019.
    10. Seifert, A., & Pleiss, J. (2012). Identification of selectivity determinants in CYP monooxygenases by modelling and systematic analysis of sequence and structure. Curr Drug Metab, 13, 197–202.
    11. Baier, J., Naumburg, T., Blumenstein, N., Jeurgens, L., Welzel, U., Do, T., Pleiss, J., & Bill, J. (2012). Bio-inspired mineralization of zinc oxide in presence of ZnO-binding peptides. Biointerface Res Appl Chem, 2, 380–391.
    12. Hutt, M., Kulschewski, T., & Pleiss, J. (2012). Molecular modelling of the mass density of single proteins. J Biomol Struct Dyn, 30, 318–327.
    13. Pleiss, J. (2012). Rational design of enzymes. In K. Drauz, H. Gröger, & O. May (Eds.), Enzyme catalysis in organic synthesis. Wiley-VCH.
    14. Widmann, M., Pleiss, J., & Oelschlaeger, P. (2012). Systematic analysis of metallo-b-lactamases using an automated database. Antimicrob Agents Ch, 56, 3481–3491.
  10. 2011

    1. Gruber, C., & Pleiss, J. (2011). Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities. J.Comput.Chem., 32, 600–606.
    2. Habeych, D., Juhl, P., Pleiss, J., Vanegas, D., Eggink, G., & Boeriu, C. (2011). Biocatalytic synthesis of polyesters from sugar-based building blocks using immobilized Candida antarctica lipase B. J Mol Catal B - Enzym, 71, 1–9.
    3. Rother, D., Kolter, G., Gerhards, T., Berthold, C., Gauchenova, E., Knoll, M., Pleiss, J., Müller, M., Schneider, G., & Pohl, M. (2011). S-selective mixed carboligation by structure-based design of the pyruvate decarboxylase from Acetobacter pasteurianus. ChemCatChem, 3, 1587–1596.
    4. Seifert, A., Antonovici, M., Hauer, B., & Pleiss, J. (2011). An efficient route to selective bio-oxidation catalysts: an iterative approach comprising modeling, diversification, and screening, based on CYP102A1. ChemBioChem, 12, 1346–1351.
    5. Sirim, D., Wagner, F., Wang, L., Schmid, R., & Pleiss, J. (2011). The Laccase  Engineering Database: a classification and analysis system for laccases and related multicopper oxidases. Database, bar006.
    6. Krone, M., Falk, M., Rehm, S., Pleiss, J., & Ertl, T. (2011). Interactive exploration of protein cavities. Comput Graph Forum, 30, 673–682.
    7. Pleiss, J. (2011). Protein design in metabolic engineering and synthetic biology. Curr.Opin.Biotech., 22, 1–7.
    8. Weber, E., Seifert, A., Antonovici, M., Geinitz, C., Pleiss, J., & Urlacher, V. (2011). Screening of a minimal enriched P450 BM3 mutant library for hydroxylation of cyclic and acyclic alkanes. Chem.Commun., 47, 944–946.
    9. Steudle, A., & Pleiss, J. (2011). Modelling of lysozyme binding to a cation exchange surface at atomic detail: the role of flexibility. Biophys.J., 100, 3016–3024.
  11. 2010

    1. Weber, E., Sirim, D., Schreiber, T., Bejoy, T., Pleiss, J., Hunger, M., Gläser, R., & Urlacher, V. (2010). Immobilization of P450 BM-3 monooxygenase on mesoporous molecular sieves with differentpore diameters. J Mol Catal B, 64, 29–37.
    2. Widmann, M., Juhl, P., & Pleiss, J. (2010). Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A. BMC Genomics, 11, 123.
    3. Sirim, D., Widmann, M., Wagner, F., & Pleiss, J. (2010). Prediction and analysis of the modular structure of cytochrome P450 monooxygenases. BMC Struct Biol, 10, 34–34.
    4. Widmann, M., Radloff, R., & Pleiss, J. (2010). The Thiamine diphosphate dependent Enzyme Engineering Database: A tool for the systematic analysis of sequence and structure relations. BMC Biochemistry, 11, 9–9.
    5. Widmann, M., Trodler, P., & Pleiss, J. (2010). The isoelectric region of proteins: a systematic analysis. PLoS One, 5, e10546–e10546.
    6. Gatti-Lafranconi, P., Natalello, A., Rehm, S., Doglia, S., Pleiss, J., & Lotti, M. (2010). Evolution of stability in a cold-active enzyme elicits specificity relaxation and highlights substrate-related effects on temperature adaptation. J Mol Biol, 395, 155–166.
    7. Trodler, P., Eiben, S., Koschorreck, K., Müller, M., Pleiss, J., Maurer, S., Branneby, C., & Schmid, R. (2010). Rational design of Pseudozyma antarctica lipase B yielding a general esterification catalyst. ChemBioChem, 11, 789–795.
    8. Liu, D., Trodler, P., Eiben, S., Koschorrek, K., Mueller, M., Pleiss, J., Maurer, S., Branneby, C., & Schmid, R. (2010). Rational Design of Pseudozyma antarctica Lipase B Yielding a General Esterification Catalyst. Chem. Bio. Chem., 11, 789–795.
    9. Rehm, S., Trodler, P., & Pleiss, J. (2010). Solvent-induced lid opening in lipases: A molecular dynamics study. Protein Sci., 19, 2122–2130.
    10. Thai, K., & Pleiss, J. (2010). SHV Lactamase Engineering Database: a reconciliation tool for SHV β-lactamases in public databases. BMC Genomics, 11, 563–563.
    11. Juhl, P., Doderer, K., Hollmann, F., Thum, O., & Pleiss, J. (2010). Engineering of Candida antarctica lipase B forhydrolysis of bulky carboxylic acid esters. J Biotechnol, 150, 474–480.
  12. 2009

    1. Seifert, A., & Pleiss, J. (2009). Identification of selectivity-determining residues in cytochrome P450 monooxygenases: a systematic analysis of the substrate recognition site 5. Proteins, 74, 1028–1035.
    2. Trodler, P., Schmid, R., & Pleiss, J. (2009). Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase. BMC Struct Biol, 9, 38.
    3. Seifert, A., Vomund, S., Grohmann, K., Kriening, S., Urlacher, V., Laschat, S., & Pleiss, J. (2009). Rational design of a minimal and highly enrichedCYP102A1 mutant library with improved regio-, stereo- and chemoselectivity. ChemBioChem, 10, 853–861.
    4. Bös, F., & Pleiss, J. (2009). Multiple molecular dynamics simulations of TEMbeta-lactamase: Dynamics and water binding of the Omega-loop. Biophys J, 97, 2550–2558.
    5. Dietrich, M., Schmid, R., Pleiss, J., & Urlacher, V. (2009). Altering the regioselectivity of the subterminal fatty acid hydroxylase P450 BM-3 towards gamma- and delta-positions. J Biotechnol, 139, 115–117.
    6. Thai, Q., Bös, F., & Pleiss, J. (2009). The Lactamase Engineering Database: a critical survey of TEM sequences in public databases. BMC Genomics, 10, 390.
    7. Chen, B., Huang, Y., Pleiss, J., & Lin, Z. (2009). Morphing activity between structurally similar enzymes: from heme-free bromoperoxidase to lipase. Biochemistry, 48, 11496–11504.
    8. Sirim, D., Wagner, F., Lisitsa, A., & Pleiss, J. (2009). The Cytochrome P450 Engineering Database: integration of biochemical properties. BMC Biochemistry, 10, 27.
    9. Juhl, P., Trodler, P., Tyagi, S., & Pleiss, J. (2009). Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking. BMC Struct Biol, 9, 39.
    10. Knoll, M., Hamm, T., Wagner, F., Martinez, V., & Pleiss, J. (2009). The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases. BMC Bioinformatics, 10, 89.
    11. Branco, R., Graber, M., Denis, V., & Pleiss, J. (2009). Molecular mechanism of the hydration of Candida antarctica lipase B in gas phase: water adsorption isotherms and molecular dynamics simulations. ChemBioChem, 10, 2913–2919.
  13. 2008

    1. Trodler, P., Nieveler, J., Rusnak, M., Schmid, R., & Pleiss, J. (2008). Rational design of a new one-step purification strategy for Candida antarctica lipase B by ion-exchange chromatography. J Chromatogr A, 1179, 161–167.
    2. Trodler, P., & Pleiss, J. (2008). Modeling structure and flexibility of Candida antarctica lipase B in organic solvents. BMC Struct Biol, 8, 9.
    3. Bidmon, K., Grottel, S., Bös, F., Pleiss, J., & Ertl, T. (2008). Visual abstractions of solvent pathlines near protein cavities. Comput Graph Forum, 27, 935–942.
    4. Knoll, M., & Pleiss, J. (2008). The Medium-Chain Dehydrogenase/Reductase Engineering Database: A systematic analysis of a diverse protein family to understand sequence-structure-function relationship. Protein Sci, 17, 1689–1697.
    5. Branco, R., Seifert, A., Budde, M., Urlacher, V., Ramos, M., & Pleiss, J. (2008). Anchoring effects in a wide binding pocket: The molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium. Proteins, 73, 597–607.
    6. Messerschmidt, S., Kolbe, A., Müller, D., Knoll, M., Pleiss, J., & Kontermann, R. (2008). Novel single-chain Fv′ formats for the generation of immunoliposomes by site-directed coupling. Bioconjugate Chem., 19, 362–369.
    7. Bös, F., & Pleiss, J. (2008). Conserved water molecules stabilize the omega-loop in class A beta-lactamases. Antimicrob Agents Chemother, 52, 1072–1079.
    8. Widmann, M., Clairo, M., Dippon, J., & Pleiss, J. (2008). Analysis of the distribution of functionally relevant rare codons. BMC Genomics, 9, 207.
    9. Gocke, D., Walter, L., Gauchenova, E., Kolter, G., Knoll, M., Berthold, C., Schneider, G., Pleiss, J., Müller, M., & Pohl, M. (2008). Rational protein design of ThDP-dependent enzymes: engineering stereoselectivity. ChemBioChem, 9, 406–412.
    10. Dietrich, M., Eiben, S., Asta, C., Pleiss, J., & Urlacher, V. (2008). Cloning, expression and characterisation of CYP102A7, a self-sufficient P450 from Bacillus licheniformis. Appl Microbiol Biotechnol, 79, 931–940.
  14. 2007

    1. Fischer, M., Knoll, M., Sirim, D., Wagner, F., Funke, S., & Pleiss, J. (2007). The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family. Bioinformatics, 23, 2015–2017.
    2. Pleiss, J. (2007). Human Cytochrome P450 Monooxygenases – a General Model of Substrate Specificity and Regioselectivity. In V. B. U. Rolf D. Schmid (Ed.), Modern Biooxidation:Enzymes, Reactions and Applications. Wiley-VCH.
    3. Klein, K., Tatzel, S., Raimundo, S., Saussele, T., Hustert, E., Pleiss, J., Eichelbaum, M., & Zanger, U. (2007). A natural variant of the heme-bindingsignature (R441C) resulting in complete loss of the function of CYP2D6. Drug Metab Dispos, 35, 1247–1250.
    4. Oelschlaeger, P., & Pleiss, J. (2007). Hydroxyl groups in the betabeta sandwich of metallo-beta-lactamases favor enzyme activity: Tyr218 and Ser262 pull down the lid. J Mol Biol, 366, 316–329.
  15. 2006

    1. Seifert, A., Tatzel, S., Schmid, R., & Pleiss, J. (2006). Multiple molecular dynamics simulations of human P450 monooxygenase CYP2C9: the molecular basis of substrate binding and regioselectivity toward warfarin. Proteins, 64, 147–155.
    2. Pleiss, J. (2006). The promise of synthetic biology. Appl Microbiol Biotechnol, 73, 735–739.
    3. Fischer, M., Thai, Q., Grieb, M., & Pleiss, J. (2006). DWARF - a data warehouse system for analyzing protein families. BMC Bioinformatics, 7, 495–495.
    4. Tyagi, S., & Pleiss, J. (2006). Biochemical profiling in silico - Predicting substrate specificities of large enzyme families. J Biotechnol, 124, 108–116.
    5. Knoll, M., Müller, M., Pleiss, J., & Pohl, M. (2006). Factors mediating activity, selectivity, and substrate specificity for the thiamin diphosphate-dependent enzymes benzaldehyde lyase and benzoylformate decarboxylase. Chembiochem, 7, 1928–1934.
  16. 2005

    1. Koschorreck, M., Fischer, M., Barth, S., & Pleiss, J. (2005). How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli. BMC Genomics, 6, 1–10.
    2. Oelschlaeger, P., Mayo, S., & Pleiss, J. (2005). Impact of remote mutations on metallo-beta-lactamase substrate specificity: implications for the evolution of antibiotic resistance. Protein Sci, 14, 765–774.
    3. Bornscheuer, U., Henke, E., & Pleiss, J. (2005). Enzymatic methods. In A. Christoffers J. Baro (Ed.), Quaternary Stereocenters (pp. 315–327). Wiley-VCH.
    4. Riepe, F., Tatzel, S., Sippell, W., Pleiss, J., & Krone, N. (2005). Congenital adrenal hyperplasia: the molecular basis of 21-hydroxylase deficiency in H-2(aw18) mice. Endocrinology, 146, 2563–2574.
  17. 2004

    1. Tejo, B., Salleh, A., & Pleiss, J. (2004). Structure and dynamics of Candida rugosa lipase: the role of organic solvent. J Mol Model, 10, 358–366.
    2. Barth, S., Fischer, M., Schmid, R., & Pleiss, J. (2004). Sequence and structure of epoxide hydrolases: a systematic analysis. Proteins, 55, 846–855.
    3. Strohmeier, M., Hrmova, M., Fischer, M., Harvey, A., Fincher, G., & Pleiss, J. (2004). Molecular modeling of family GH16 glycoside hydrolases: potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the poaceae. Protein Sci, 13, 3200–3213.
    4. Schmid, R., Pleiss, J., & Urlacher, V. (2004). Biokatalyse: Selektivoxidation von C-H-Bindungen mit O2. Nachr Chem, 52, 767–772.
    5. Richter, T., Muerdter, T., Heinkele, G., Pleiss, J., Tatzel, S., Schwab, M., Eichelbaum, U., & Zanger, M. (2004). Potent mechanism-based inhibition of human CYP2B6 by clopidogrel and ticlopidine. J Pharmacol Exp Ther, 303, 189–197.
    6. Barth, S., Fischer, M., Schmid, R., & Pleiss, J. (2004). The database of epoxide hydrolases andhaloalkane dehalogenases: one structure, manyfunctions. Bioinformatics, 20, 2845–2847.
    7. Currle-Linde, N., Boes, F., Lindner, P., Pleiss, J., & Resch, M. (2004). A Management System for Complex Parameter Studies and Experiments in Grid Computing. In T. Gonzales (Ed.), Proceedings of the 16th IASTED International Conference on PDCS - International Conference on Parallel and Distributed Computing and Systems (pp. 34–39). Acta press.
  18. 2003

    1. Oelschlaeger, P., Schmid, R., & Pleiss, J. (2003). Insight into the mechanism of the IMP-1 metallo-beta-lactamase by molecular dynamics simulations. Protein Eng, 16, 341–350.
    2. Henke, E., Bornscheuer, U., Schmid, R., & Pleiss, J. (2003). A molecular mechanism of enantiorecognition of tertiary alcohols by carboxylesterases. ChemBioChem, 4, 485–493.
    3. Oelschlaeger, P., Schmid, R., & Pleiss, J. (2003). Modeling domino effects in enzymes: molecular basis of the substrate specificity of the bacterial metallo-beta-lactamases IMP-1 and IMP-6. Biochemistry, 42, 8945–8956.
    4. Fischer, M., & Pleiss, J. (2003). The Lipase Engineering Database: a navigation and analysis tool for protein families. Nucleic Acids Res, 31, 319–321.
    5. Lich, N., Barth, F., Pleiss, J., & Hai, T. (2003). Homology modelling of alpha-amylase from Saccharomycopsis fibuligera with maltohexaose substrate. Vietnam Journal of Biotechnology, 1, 149–159.
  19. 2002

    1. Henke, E., Pleiss, J., & Bornscheuer, U. (2002). Activity of lipases and esterases towards tertiary alcohols: insights into structure-function relationships. Angew Chem Int Ed, 41, 3211–3213.
    2. Gentner, C., Schmid, R., & Pleiss, J. (2002). Primary alcohols in a ring structure: quantifying enantioselectivity of Pseudomonas cepacia lipase by an in silico assay. Colloids Surf B Biointerfaces, 26, 57–66.
    3. Bathelt, C., Schmid, R., & Pleiss, J. (2002). Regioselectivity of CYP2B6: homology modeling, molecular dynamics simulation, docking. J Mol Model, 8, 327–335.
    4. Kusharyoto, W., Pleiss, J., Bachmann, T., & Schmid, R. (2002). Mapping of a hapten-binding site: molecular modeling and site-directed mutagenesis study of an anti-atrazine antibody. Protein Eng, 15, 233–241.
    5. Schmitt, J., Brocca, S., Schmid, R., & Pleiss, J. (2002). Blocking the tunnel: engineering of Candida rugosa lipase mutants with short chain length specificity. Protein Eng, 15, 595–601.
  20. 2001

    1. Schwaneberg, U., Fischer, M., Schmitt, J., Pleiss, J., Lutz-Wahl, S., & Schmid, R. (2001). Rational evolution of a medium chain-specific cytochrome P-450 BM-3 variant. Biochim Biophys Acta, 1545, 114–121.
    2. Schulz, T., Schmid, R., & Pleiss, J. (2001). Structural basis of stereoselectivity in Candida rugosa lipase-catalyzed hydrolysis of secondary alcohols. J Mol Model, 7, 265–270.
    3. Kahlow, U., Schmid, R., & Pleiss, J. (2001). A model of the pressure dependence of the enantioselectivity of Candida rugosa lipase towards (±)-menthol. Protein Sci, 10, 1942–1952.
    4. Bachmann, T., Pleiss, J., Villatte, F., & Schmid, R. (2001). Bioresponse-Linked Analysis Based on Acetylcholinesterase Inhibition. In H. B (Ed.), Bioresponse-Linked Instrumental Analysis. B.G. Teubner.
  21. 2000

    1. Pleiss, J., Fischer, M., Peiker, M., Thiele, C., & Schmid, R. (2000). Lipase Engineering Database: understanding and exploiting sequence-structure-function relationships. J Mol Catal B: Enzym, 10, 491–508.
    2. Pleiss, J., Scheib, H., & Schmid, R. (2000). The his gap motif in microbial lipases: a determinant of stereoselectivity toward triacylglycerols and analogs. Biochimie, 82, 1043–1052.
    3. Bornscheuer, U., Pleiss, J., Schmidt-Dannert, C., & Schmid, R. (2000). Lipases from Rhizopus species: genetics, structure and applications. In L. Alberghina (Ed.), Protein engineering in industrial biotechnology (pp. 115–134). CRC Press.
    4. Pleiss, J., Fischer, M., Scheib, H., Schulz, T., & Schmid, R. (2000). Modelling structure-function relationship of lipase binding sites-a case study of specificity and selectivity. In G. Kokotos (Ed.), Lipases and LipidsStructure, function and biotechnological applications (pp. 21–39). Crete University Press.
    5. Schulz, T., Pleiss, J., & Schmid, R. (2000). Stereoselectivity of Pseudomonas cepacia lipase towards secondary alcohols: a quantitative model. Protein Sci, 9, 1053–1062.
    6. Pleiss, J. (2000). In silico-Assays: Computergestuetzte Modellierung der Stereoselektivität von Lipasen. Transkript, 9, 38–40.
    7. Otto, R., Scheib, H., Bornscheuer, U., Pleiss, J., Syldatk, C., & Schmid, R. (2000). Substrate specificity of lipase B from Candida antarctica in the synthesis of arylaliphatic glycolipids. J Mol Catal B Enzym, 8, 201–211.
    8. Kovac, A., Scheib, H., Pleiss, J., Schmid, R., & Paltauf, F. (2000). Molecular basis of lipase stereoselectivity. Eur J Lipid Sci Tech, 102, 61–77.
    9. Hwang, B., Scheib, H., Pleiss, J., Kim, B., & Schmid, R. (2000). Computer-aided molecular modeling of the enantioselectivity of Pseudomonas cepacia lipase toward g- and d-lactones. J Mol Catal B Enzym, 10, 223–231.
  22. 1999

    1. Pleiss, J., & Schmid, R. (1999). Bioinformatics and the internet. Chemistry International, 21, 33–36.
    2. Scheib, H., Pleiss, J., Kovac, A., Paltauf, F., & Schmid, R. (1999). Stereoselectivity of Mucorales lipases toward triradylglycerols--a simple solution to a complex problem. Protein Sci, 8, 215–221.
    3. Pleiss, J., Mionetto, N., & Schmid, R. (1999). Probing the acyl binding site of acetylcholinesterase by protein engineering. J Mol Catal B: Enzym, 6, 287–296.
  23. 1998

    1. Schmidt-Dannert, C., Pleiss, J., & Schmid, R. (1998). A toolbox of recombinant lipases for industrial applications. Ann N Y Acad Sci, 864, 14–22.
    2. Mindermann, A., Pleiss, J., & Hülser, D. (1998). Molecular Modeling of Gap Junction Pores. In R. Werner (Ed.), Gap Junctions. Proceedings of the 8th International Gap Junction Conference, Key Largo, Florida (pp. 67–71). IOS Press.
    3. Hülser, D., Eckert, R., Irmer, U., Krisciukaitis, A., Mindermann, A., Pleiss, J., Rehkopf, B., Sharovskaya, J., & Traub, O. (1998). Intercellular communication via gap junction channels. Bioelectrochem Bioenerg, 45, 55–65.
    4. Scheib, H., Pleiss, J., Stadler, P., Kovac, A., Potthoff, A., Haalck, L., Spener, F., Paltauf, F., & Schmid, R. (1998). Rational design of Rhizopus oryzae lipase with modified stereoselectivity toward triradylglycerols. Protein Eng, 11, 675–682.
    5. Drees, R., Pleiss, J., Schmid, R., & Roller, D. (1998). Integrating molecular modeling tools and virtual reality engines: an architecture for a highly immersive molecular modeling (HIMM) environment. Proceedings of CGI, 391–392.
    6. Pleiss, J., Fischer, M., & Schmid, R. (1998). Anatomy of lipase binding sites: the scissile fatty acid binding site. Chem Phys Lipids, 93, 67–80.
    7. Otto, R., Bornscheuer, U., Scheib, H., Pleiss, J., Syldatk, C., & Schmid, R. (1998). Lipase-catalyzed esterification of unusual substrates: synthesis of glucuronic acid and ascorbic acid. Biotechnol Lett, 20, 1091–1094.
  24. 1997

    1. Haalck, L., Paltauf, F., Pleiss, J., Schmid, R., Spener, F., & Stadler, P. (1997). Stereoselectivity of lipase from Rhizopus oryzae toward triacylglycerols and anlogs: computer aided modelling and experimental validation. Methods Enzymol, 284, 353–376.
    2. Pleiss, J., Mionetto, N., & Schmid, R. (1997). Protein engineering of rat brain acetylcholinesterase: a point mutation enhances sensitivityto pesticides. Protein Eng, 10, 66–66.
    3. Weber, H., Zuegg, J., Faber, J., & Pleiss, J. (1997). Molecular reasons for lipase-sensitivity against acetaldehyde. J Mol Catal B: Enzym, 3, 131–138.
    4. Holzwarth, H.-C., Pleiss, J., & Schmid, R. (1997). Computer-aided modelling of stereoselective triglyceride hydrolysis catalyzed by Rhizopus oryzae lipase. J Mol Catal B Enzym, 3, 73–82.
  25. 1996

    1. Drees, R., Pleiss, J., & Schmid, R. (1996). Highly immersive molecular modeling (HIMM): an architecture for the integration of molecular modelling and virtual reality. In R. Hofestädt, M. Löffler, & D. Schomburg (Eds.), Computer science and biology : proceedings of the German Conference on Bioinformatics (GCB 96) (pp. 190–192). Universität Leipzig.
  26. 1994

    1. Pleiss, J. (1994). Quantitative modelling of lipase enantioselectivity. In A. Svendsen (Ed.), Enzyme functionality: Design, engineering, and screening. Marcel Dekker.
    2. Pleiss, J. (1994). Molecular basis of specificity and stereoselectivity of microbial lipases toward triacylglycerols. In U. T. Bornscheuer (Ed.), Enzymes in Lipid Modification (pp. 85–99). Wiley-VCH.
  27. 1992

    1. Pleiss, J., & Jähnig, F. (1992). Conformational transition of an alpha-helix studied by molecular dynamics. Eur Biophys J, 21, 63–70.
  28. 1991

    1. Pleiss, J., & Jähnig, F. (1991). Collective vibrations of an alpha-helix. A molecular dynamics study. Biophys J, 59, 795–804.
  29. 1989

    1. Roditi, I., Schwarz, H., Pearson, T., Beecroft, R., Liu, M., Richardson, J., Bühring, H., Pleiss, J., Bülow, R., & et, al. (1989). Procyclin gene expression and loss of the variant surface glycoprotein during differentiation of Trypanosoma brucei. J Cell Biol, 108, 737–746.
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