In Search of the Prototype of Nitric Oxide Synthase - Zemojtel, Tomasz; Wade, Rebecca C.; Dandekar, Thomas (FEBS Letts., 2003)

Inhibitor specificity via protein dynamics: Insights from design of antibacterial agents targeted against thymidylate synthase - Ferrari, Stefania; Costi, Paola M; Wade, Rebecca C. (Chemistry & Biology, 2003)

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 - Bertoša, Branimir; Kojić-Prodić, Biserka; Wade, Rebecca C.; Ramek, Michael; Piperaki, Stavroula; Tsantili-Kakoulidou, Anna; Tomić, Sanja (Chem. Inf. Comput. Sci., 2003)

What Determines the Redox Potential of Ferredoxins? - Essigke, Timm; Ullmann, G. Matthias; Wade, Rebecca C. (2003)

Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations - Kmuníček, Jan; Boháč, Michal; Luengo, Santos; Gago, Federico; Wade, Rebecca C.; Damborský, Jiří (J. Comput. Aided Mol. Des., 2003)

MolSurfer: a macromolecular interface navigator - Gabdoulline, Razif; Wade, Rebecca C.; Walther, Dirk (Nucleic Acids Res., 2003)

Concerted Simulations Reveal How Peroxidase Compound III Formation Results in Cellular Oscillations - Gabdoulline, Razif R.; Kummer, Ursula; Olsen, Lars F.; Wade, Rebecca C. (Biophys. J., 2003)

ProSAT: Functional annotation of protein 3D structures - Gabdoulline, R. R.; Hoffmann, R.; Leitner, F.; Wade, Rebecca C. (Bioinformatics, 2003)

DSMM - a Database of Simulated Molecular Motions - Finocchiaro, Giacomo; Wang, Ting; Hoffmann, Rene; Gonzalez, Aitor; Wade, Rebecca C. (Nucleic Acids Res., 2003)

Implicit Solvent Models for Flexible Protein-protein Docking by Molecular Dynamics Simulation - Wang, Ting; Wade, Rebecca C. (Proteins, 2003)

Specific and Non-specific Effects of Potassium Cations on Substrate-protein Interactions in Cytocromes P450cam and P450lin - Deprez, Eric; Gill, Edward; Helms, Volkhard; Wade, Rebecca C.; Hui Bon Hoa, Gaston (J. Inorg. Biochem., 2002)

Comparative Binding Energy (COMBINE) Analysis of OppA−Peptide Complexes to Relate Structure to Binding Thermodynamics - Wang, Ting; Wade, Rebecca C. (Journal of Medicinal Chemistry, 2002)

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 - Winn, P. J.; Ludemann, S. K.; Gauges, R.; Lounnas, V.; Wade, Rebecca C. (Proc. Natl. Acad. Sci. USA, 2002)

Biomolecular diffusional association - Gabdoulline, Razif R.; Wade, Rebecca C. (Curr. Opin. Struct. Biol., 2002)

Elusive recognition determinants for ubiquitination - Banerjee, Amit; Wade, Rebecca C. (J. Molec. Recogn., 2002)

Biologically relevant properties of copper-containing proteins analysed by means of semi-quantitative and quantitative theoretical descriptors - Rienzo, Francesca De; Gabdoulline, Razif R.; Wade, Rebecca C.; Menziani, M. Cristina (2002)

Hits and Lead Discovery in the Identification of New Drugs against the Trypanosomatidic Infections - Calogeropoulou, Theodora; Magoulas, George E.; Pöhner, Ina; Panecka-Hofman, Joanna; Linciano, Pasquale; Ferrari, Stefania; Santarem, Nuno; Jiménez-Antón, M. Dolores; Olías-Molero, Ana Isabel; Alunda, José María; Silva, Anabela Cordeiro da; Wade, Rebecca C.; et al. (2019)

A genetic screen pinpoints ribonucleotide reductase residues that sustain dNTP homeostasis and specifies a highly mutagenic type of dNTP imbalance - Schmidt, Patrick; Sharma, Sushma; Reyes, Gloria X; Gries, Kerstin; Gross, Maike; Zhao, Boyu; Yuan, Jui-Hung; Wade, Rebecca C.; Chabes, Andrei; Hombauer, Hans (Nucleic Acids Research, 2019)

Computing Protein-Ligand Binding Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics Simulations - Sadiq, Kashif; Wade, Rebecca C. (Biophysical Journal, 2018)

Proceedings of the International School of Physics "Enrico Fermi" workshop on Protein Folding and Drug Design - Winn, P.J.; Zahran, M.; Wade, Rebecca C. (2007)

The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration - Gdynia, Georg; Sauer, Sven W.; Kopitz, Jürgen; Fuchs, Dominik; Duglova, Katarina; Ruppert, Thorsten; Miller, Matthias; Pahl, Jens; Cerwenka, Adelheid; Enders, Markus; Mairbäurl, Heimo; Kamiński, Marcin M.; et al. (Nature Communications, 2016)

Ten Simple Rules for Organizing an Unconference - Budd, Aidan; Dinkel, Holger; Corpas, Manuel; Fuller, Jonathan C.; Rubinat, Laura; Devos, Damien P.; Khoueiry, Pierre H.; Förstner, Konrad U.; Georgatos, Fotis; Rowland, Francis; Sharan, Malvika; Binder, Janos X.; et al. (PLOS Computational Biology, 2015)

A Quick Guide for Building a Successful Bioinformatics Community. - Budd, Aidan; Corpas, Manuel; Brazas, Michelle D.; Fuller, Jonathan C.; Goecks, Jeremy; Mulder, Nicola J.; Michaut, Magali; Ouellette, B. F. Francis; Pawlik, Aleksandra; Blomberg, Niklas (PLoS computational biology, 2015)
"Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop "The ’How To Guide’ for Establishing a Successful Bioinformatics Network" at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).

Biggest challenges in bioinformatics - Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen (EMBO reports, 2013)
The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the ‘Biggest Challenges in Bioinformatics’ in a ‘World Café’ style event.

Das biomolekulare Erkennungspuzzle - Wade, Rebecca C. (Spektrum der Wissenschaft - Extra, 2011)

Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning - Baar, Ivo; Hubner, Lukas; Oettig, Peter; Zapletal, Adrian; Schlag, Sebastian; Stamatakis, Alexandros; Morel, Benoit (2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2019)

From Brazil to Germany: Challenges and Advantages - Nunes Alves, Ariane (Journal of Chemical Information and Modeling, 2019)

FTIR studies of the redox partner interaction in cytochrome P450: The Pdx-P450cam couple - Karyakin, A.; Motiejunas, D.; Wade, Rebecca C.; Jung, C. (Biochimica et Biophysica Acta. General Subjects, 2007)

Beilstein Proceedings of the 2nd Conference on ’Experimental Standard Conditions of Enzyme Characterizations (ESCEC)’ \em Ruedesheim (2007) \em - Stein, M.; Gabdoulline, R.R.; Beßon, B.; Wade, Rebecca C. (2006)

Characterization of Protein- Binding Sites and Ligands Using Molecular Interaction Fields - Cruciani, G.; Carosati, E.; Wade, Rebecca C.; Baroni, M. (2006)

Structural, Energetic and Dynamic Aspects of Ligand-Receptor Interactions - Motiejunas, D.; Wade, Rebecca C. (2006)

From Computational Biophysics to Systems Biology 2006 - Stein, M.; Gabdoulline, R.R.; Wade, Rebecca C. (2006)

Force Field Effects on a b-sheet Protein Domain Structure in Thermal Unfolding Simulations - Wang, T.; Wade, Rebecca C. (J Chem Theory and Comput, 2006)

Pushing the limits: Editorial Overview. Curr - McCammon, J.A.; Wade, Rebecca C. (Opin. Struct. Biol., 2005)

Proceedings of the 13\textsuperscriptth International Conference on Cytochromes P450 - Essigke, T.E.; Ullmann, M.; Wade, Rebecca C. (2003)

Electrostatic Analysis and Brownian Dynamics Simulation of the Association of Plastocyanin and Cytochrome F - De Rienzo, Francesca; Gabdoulline, Razif R.; Menziani, M. Cristina; De Benedetti, Pier G.; Wade, Rebecca C. (Biophys. J., 2001)

Comparative Binding Energy (COMBINE) Analysis of the Substrate Specificity of Haloalkane Dehalogenase from Xanthobacter Autotrophicus GJ10 - Kmuníček, Jan; Luengo, Santos; Gago, Federico; Ortiz, Angel Ramirez; Wade, Rebecca C.; Damborský, Jiří (Biochemistry, 2001)

Comparative Binding Energy (COMBINE) analysis of Influenza Neuraminidase-Inhibitor Complexes - Wang, Ting; Wade, Rebecca C. (J. Med. Chem., 2001)

Protein-protein Association: Investigation of Factors Influencing Association Rates by Brownian Dynamics Simulations - Gabdoulline, Razif R.; Wade, Rebecca C. (J. Mol. Biol., 2001)

Substrate access to cytochrome P450cam investigated by molecular dynamics simulations: An interactive look at the underlying mechanisms - Luedemann, S.K.; Gabdoulline, R.R.; Lounnas, V.; Wade, Rebecca C. (Internet. J. Chem., 4, 6, 2001)

Protein Interaction Property Similarity Analysis - Wade, Rebecca C.; Gabdoulline, R. R.; De Rienzo, F. (Intl. J. Quant. Chem., 2001)

COMBINE Analysis of Nuclear Receptor-DNA Binding Specificity: Comparison of Two Data Sets - Tomic, S.; Wade, Rebecca C. (Croat. Chem. Acta., 2001)

Protein-Protein Docking - Ehrlich, Lutz P.; Wade, Rebecca C. (Rev. Comp. Chem., 2001)

A Comparison of Aqueous Solvent Models Used in the Calculation of the Raman and ROA spectra of L-alanine - Jalkanen, K.J; Nieminen, R.M; Frimand, K; Bohr, J; Bohr, H; Wade, Rebecca C.; Tajkhorshid, E; Suhai, S (Chem. Phys., 2001)

COMBINE 3D-QSAR analysis of Influenza Neuraminidase Inhibitors - Wang, T.; Wade, Rebecca C. (2001)

Derivation of QSARs using 3D Structural Models of Protein-ligand complexes by COMBINE Analysis - Wade, Rebecca C. (2001)

How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics to investigate ligand access channels and mechanisms - Lüdemann, Susanna K; Lounnas, Valère; Wade, Rebecca C. (J. Mol. Biol., 2000)

How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways - Lüdemann, Susanna K.; Lounnas, Valère; Wade, Rebecca C. (J. Mol. Biol., 2000)

Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam - Das, Bedamati; Helms, Volkhard; Lounnas, Valère; Wade, Rebecca C. (J. Inorg. Biochem., 2000)

Blue Copper Proteins: A Comparative Analysis of their Molecular Interaction Properties - De Rienzo, F.; Gabdoulline, R.R.; Menziani, M. C.; Wade, Rebecca C. (Protein Science, 2000)

The cisProline(i-1)-Aromatic(i) Interaction: Folding of the Ala-cisPro-Tyr peptide characterized by NMR and theoretical approaches - Nardi, Frederico; Kemmink, Johan; Sattler, Michael; Wade, Rebecca C. (J. Biomol. NMR, 2000)

pKa calculations for class C beta-lactamases: The role of tyr-150 - Lamotte-Brasseur, Josette; Dubus, Alain; Wade, Rebecca C. (Proteins: Structure, Function, and Genetics, 2000)

Nuclear receptor-DNA binding specificity: a COMBINE and Free-Wilson QSAR analysis - Tomic, Sanja; Nilsson, Lennart; Wade, Rebecca C. (J. Med. Chem., 2000)

COMBINE and Free-Wilson QSAR analysis of nuclear receptor - DNA binding - Tomić, Sanja; Nilsson, Lennart; Wade, Rebecca C. (2000)

MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes - Gabdoulline, R.R.; Wade, Rebecca C.; Walter, D. (Trends in Biochem. Sci., 1999)

Improving macromolecular electrostatics calculations - Nielsen, J. E.; Andersen, K. V.; Honig, B.; Hooft, R. W. W.; Klebe, G.; Vriend, G.; Wade, Rebecca C. (Protein Eng, 1999)

Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase-Fasciculin - Elcock, Adrian H; Gabdoulline, Razif R; Wade, Rebecca C.; McCammon, J.Andrew (J. Mol. Biol., 1999)

Stability of the beta-sheet of the WW domain: A Molecular Dynamics Simulation Study - Ibragimova, Gulshat T.; Wade, Rebecca C. (Biophys. J., 1999)

Docking of Glycosaminoglycans to Heparin-binding Proteins: Validation for aFGF, bFGF and Antithrombin and Application to IL-8 - Bitomsky, Wolfgang; Wade, Rebecca C. (J. Am. Chem. Soc., 1999)

Towards molecular dynamics simulations of large proteins with a hydration shell at constant presssure - Lounnas, Valère; Lüdemann, Susanna K.; Wade, Rebecca C. (Biophys. Chem., 1999)

pKa calculations for class A beta-lactamases: influence of substrate binding - Lamotte-Brasseur, Josette; Lounnas, Valère; Raquet, Xavier; Wade, Rebecca C. (Protein Sci, 1999)

Ways and Means to Enhance the Configurational Sampling of Small Peptides in Aqueous Solution in Molecular Dynamics Simulations - Nardi, F.; Wade, Rebecca C. (1999)

L-Alanyl-L-alanine in the zwitterionic state: structures determined in the presence of explicit water molecules and with continuum models using density functional theory - Knapp-Mohammady, M; Jalkanen, K.J; Nardi, F; Wade, Rebecca C.; Suhai, S (Chemical Physics, 1999)

Comparative Kinetic Analysis of FLP and Cre Recombinases: Mathematical Models for DNA Binding and Recombination - Ringrose, Leonie; Lounnas, Valere; Ehrlich, Lutz; Buchholz, Frank; Wade, Rebecca C.; Stewart, A.Francis (J. Mol. Biol., 1998)

Use of Multiple Molecular Dynamics Trajectories to Study Biomolecules in Solution: The YTGP Peptide - Worth, Graham A.; Nardi, Frederico; Wade, Rebecca C. (J. Phys. Chem., 1998)

Electrostatic steering and ionic tethering in enzyme-ligand binding: Insights from simulations - Wade, Rebecca C.; Gabdoulline, R. R.; Ludemann, S. K.; Lounnas, V. (Proc. Natl. Acad. Sci. USA, 1998)

Classification of auxin related compounds based on similarity of their interaction fields: Extension to a new set of compounds - Tomic, S.; Gabdoulline, R.R.; Kojic-Prodic, B.; Wade, Rebecca C. (Internet J. Chem., 1998)

Importance of explicit salt ions for protein stability in molecular dynamics simulation - Ibragimova, Gulshat T.; Wade, Rebecca C. (Biophys. J., 1998)

Computational Alchemy to Calculate Absolute Protein-Ligand Binding Free Energy - Helms, Volkhard; Wade, Rebecca C. (J. Am. Chem. Soc., 1998)

Brownian Dynamics - Madura, Jeffry D.; Briggs, James M.; Wade, Rebecca C.; Gabdoulline, Razif R. (1998)

Classification of auxin plant hormones by interaction property similarity indices - Tomić, Sanja; Gabdoulline, Razif R.; Kojić-Prodić, Biserka; Wade, Rebecca C. (J. Comput. Aided Mol. Des., 1998)

Prediction of protein hydration sites from sequence by modular neural networks - Ehrlich, L.; Reczko, M.; Bohr, H.; Wade, Rebecca C. (Protein Eng., 1998)

Brownian Dynamics Simulation of Protein–Protein Diffusional Encounter - Gabdoulline, Razif R.; Wade, Rebecca C. (Methods, 1998)

Computational Strategies for Modeling Receptor Flexibility in Studies of Receptor-Ligand Interactions - Wade, Rebecca C.; Lüdemann, S. (Structure-Based Drug Design, 1998)

Computational Approaches to Modeling Receptor Flexibility Upon Ligand Binding: Application to Interfacially Activated Enzymes - Wade, Rebecca C.; Sobolev, V.; Ortiz, A. R.; Peters, G. (Structure-Based Drug Design, 1998)

’Flu’ and Structure Based Drug Design - Wade, Rebecca C. (Structure, 1997)

pKa Calculations for Class A Beta-lactamases: Methodological and Mechanistic Implications - Raquet, X.; Lounnas, V.; Lamotte-Brasseur, J.; Frère, J.M.; Wade, Rebecca C. (Biophys. J., 1997)

CASP2 molecular docking predictions with the LIGIN software - Sobolev, Vladimir; Moallem, Theodore M.; Wade, Rebecca C.; Vriend, Gert; Edelman, Marvin (Proteins, 1997)

Substrate Access to Cytochrome P450cam: a Comparison of a Thermal Motion Pathway Analysis with Molecular Dynamics Simulation Data - Lüdemann, Susanna K.; Carugo, Oliviero; Wade, Rebecca C. (J. Mol. Model., 1997)

Local interactions of aromatic residues in short peptides in aqueous solution: a combined database and energetic analysis - Nardi, Frederico; Worth, Graham A; Wade, Rebecca C. (Folding & Design, 1997)

Exceptionally stable salt-bridges in cytochrome P450cam have functional roles - Lounnas, Valère; Wade, Rebecca C. (Biochemistry, 1997)

Simulation of the Diffusional Association of Barnase and Barstar - Gabdoulline, R.R.; Wade, Rebecca C. (Biophys. J., 1997)

Reliability of CoMFA Models: Effects of Data Scaling and Variable Selection Using a Set of Human Synovial Fluid Phospholipase A2 Inhibitors - Ortiz, Angel R.; Pastor, Manuel; Palomer, Albert; Cruciani, Gabriele; Gago, Federico; Wade, Rebecca C. (J. Med. Chem., 1997)

Free energies of hydration from thermodynamic integration: A comparison of molecular mechanics force fields and evaluation of calculations accuracy - Helms, V.; Wade, Rebecca C. (J. Comp. Chem., 1997)

Analytically defined surfaces to analyze molecular interaction properties - Gabdoulline, R.R.; Wade, Rebecca C. (J. Mol. Graph., 1996)

Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins - Demchuk, Eugene; Wade, Rebecca C. (J. Phys. Chem., 1996)

Influence of glycosylation on the activity of rG-CSFs: in vitro studies: molecular structure and modeling - Wade, Rebecca C.; Oschkinat, H. (Intl. J. Hematology, 1996)

Structural Changes in cytochrome P-450cam effected by the binding of the enantiomers (1R)-Camphor and (1S)-Camphor - Schulze, Heike; Hui Bon Hoa, Gaston; Helms, Volkhard; Wade, Rebecca C.; Jung, Christiane (Biochemistry, 1996)

Fundamentals of Enzyme-Ligand Interactions in Cytochrome P450cam - Wade, Rebecca 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.; et al. (1996)

TRAJAN: A Tool to Analyze Trajectories from Molecular Simulations - Worth, Graham A.; Lecuyer, Christophe; Wade, Rebecca C. (J. Mol. Graph., 1996)

Theoretical investigation of the dynamics of the Active Site Lid in Rhizomucor Miehei Lipase - Peters, G.H.; Olsen, O.H.; Svendsen, A.; Wade, Rebecca C. (Biophys. J., 1996)

Molecular Docking Using Surface Complementarity - Sobolev, V.; Wade, Rebecca C.; Vriend, G.; Edelman, M. (Proteins, 1996)

Effective charges for Macromolecules in Solvent - Gabdoulline, R. R.; Wade, Rebecca C. (J. Phys. Chem., 1996)

Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket - Helms, Volkhard; Deprez, Eric; Gill, Edward; Barret, Christel; Hui Bon Hoa, Gaston; Wade, Rebecca C. (Biochemistry, 1996)

Brownian dynamics simulations of enzyme-substrate encounter - Wade, Rebecca C. (Biochem. Soc. Trans., 1996)

Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis: Application to Human Synovial Fluid Phospholipase A2 Inhibitors - Ortiz, A.R.; Pisabarro, M.T.; Gago, F.; Wade, Rebecca C. (1995)

Aromatic - (i+2) Amine Interaction in Peptides - Worth, Graham A.; Wade, Rebecca C. (J. Phys. Chem., 1995)

Simulation of enzyme-substrate interactions: the diffusional encounter step. - Wade, R. C. (Acta Biochim Pol, 1995)
Enzymes are targets for structure-based redesign and drug design. One potentially important design strategy is to create molecules--enzymes and ligands--with desired diffusional encounter properties. Rates of diffusive bimolecular encounter can be calculated by Brownian dynamics simulation. This methodology and its application to study the factors influencing the rates of diffusion-influenced enzymes are described here.
Keywords: Diffusion; Enzymes/chemistry/*metabolism; Substrate Specificity

Molecular Dynamics Study of Short Peptide Sequences from BPTI displaying aromatic-amide interactions - Worth, G.; Wade, Rebecca C. (1995)

De novo design of ligands to block substrate access to cytochrome P450cam - Degenhardt, M.; Wade, Rebecca C. (J. Mol. Model., 1995)

Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program - Madura, Jeffry D.; Briggs, James M.; Wade, Rebecca C.; Davis, Malcolm E.; Luty, Brock A.; Ilin, Andrew; Antosiewicz, Jan; Gilson, Michael K.; Bagheri, Babak; Scott, L.Ridgway; McCammon, J.Andrew (Comp. Phys. Comm., 1995)

Thermodynamics of Water Mediating Protein-Ligand Interactions in Cytochrome P450cam: A Molecular Dynamics Study - Helms, V.; Wade, Rebecca C. (Biophys. J., 1995)

Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis - Ortiz, Angel R.; Pisabarro, M. Teresa; Gago, Federico; Wade, Rebecca C. (J. Med. Chem., 1995)

Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations - Madura, Jeffry D.; Davist, Malcolm E.; Gilson, Michael K.; Wade, Rebecca C.; Luty, Brock A.; McCammon, J. Andrew (Comp. Chem. Rev., 1994)

Rational Drug Design: GRID- and LUDI-based Structural Modifications of a Human Synovial Fluid Phospholipase A2 Inhibitor Leading to Enhanced Activity. - Pisabarro, M.T.; Palomer, A.; Ortiz, A.R.; Wade, Rebecca C.; Gago, F.; Mauleón, D.; Carganico, G. (J. Mol. Graph., 1994)

Simulation of Enzyme-Substrate Encounter with Gated Active Sites - Wade, Rebecca C.; Luty, Brock A.; Demchuk, Eugene; Madura, Jeffry D.; Davis, Malcolm E.; Briggs, James M.; McCammon, J. Andrew (Nature Struct. Biol., 1994)

Rational Modification of Human Synovial Fluid Phospholipase A2 Inhibitors - Pisabarro, M. Teresa; Ortiz, Angel R.; Palomer, Albert; Cabre, Francesc; Garcia, Luisa; Wade, Rebecca C.; Gago, Federico; Mauleon, David; Carganico, Germano (J. Med. Chem., 1994)

Receptor binding properties of four-helix-bundle growth factors deduced from electrostatic analysis - Demchuk, Eugene; Mueller, Thomas; Oschkinat, Hartmut; Sebald, Walter; Wade, Rebecca C. (Protein Science, 1994)

Homology Modeling of the Abl-SH3 domain - Pisabarro, M. T.; Ortiz, A. R.; Serrano, L.; Wade, Rebecca C. (Proteins, 1994)

Brownian Dynamics Simulations of Diffusional Encounters between Triose Phosphate Isomerase and Glyceraldhyde Phosphate: Electrostatic Steering of Glyceraldehyde Phosphate - Luty, Brock A.; Wade, Rebecca C.; Madura, Jeffry D.; Davis, Malcolm E.; Briggs, James M.; McCammon, J. Andrew (J. Phys. Chem., 1993)

Gating of the Active Site of Triose Phosphate Isomerase: Brownian Dynamics Simulations of Flexible Peptide Loops in the Enzyme - Wade, Rebecca C.; Davis, M.E.; Luty, B.A.; Madura, J.D.; McCammon, J.A. (Biophys. J., 1993)

Further Development of Hydrogen-Bond Functions for Use in Determining Energetically Favorable Binding Sites on Molecules of Known Structure. 1. Ligand Probe Groups with the Ability To Form Two Hydrogen Bonds - Wade, Rebecca C.; Clark, Kevin J.; Goodford, Peter J. (J. Med. Chem., 1993)

Further Development of Hydrogen-Bond Functions for Use in Determining Energetically Favorable Binding Sites on Molecules of Known Structure. 2. Ligand Probe Groups with the Ability To Form More Than Two Hydrogen Bonds - Wade, Rebecca C.; Goodford, Peter J. (J. Med. Chem., 1993)

Modeling three-dimensional structure and electrostatics of alkali-stable cyclomaltodextrin glucanotransferase - Demchuk, E.; Vihinen, M.; Wade, Rebecca C.; Korpela, T. (1993)

Use of neural networks to predict hydration sites in proteins - Wade, Rebecca C.; Bohr, H.; Wolynes, P.G. (1993)

Molecular Interaction Fields - Wade, Rebecca C. (1993)

Binding of an Antiviral Agent to a Sensitive and a Resistant Human Rhinovirus. Computer Simulations Studies with Sampling of Amino Acid Side-chain Conformations. I Mapping the Rotamers of Residue 188 of Viral Protein 1 - Wade, Rebecca C.; McCammon, J.Andrew (J. Mol. Biol., 1992)

Binding of an Antiviral Agent to a Sensitive and a Resistant Human Rhinovirus. Computer Simulations Studies with Sampling of Amino Acid Side-chain Conformations. II. Calculations of Free-energy Differences by Thermodynamic Integration - Wade, Rebecca C.; McCammon, J.Andrew (J. Mol. Biol., 1992)

Prediction of Water Binding Sites on Proteins by Neural Networks - Wade, Rebecca C.; Bohr, Henrik; Wolynes, Peter G. (J. Am. Chem. Soc., 1992)

A Molecular Dynamics Study of Thermodynamic and Structural Aspects of the Hydration of Cavities in Proteins - Wade, Rebecca C.; Mazor, Michael H.; McCammon, J. Andrew; Quiocho, Florante A. (Biopolymers, 1991)

An Approach to the Design of Anti-Influenza Agents - Wade, Rebecca C. (1990)

Solvation of the Active Site of Cytochrome P450-cam - Wade, Rebecca C. (J. Comp. Aided Mol. Des., 1990)

Hydration of Cavities in Proteins: a Molecular Dynamics Approach - Wade, Rebecca C.; Mazor, Michael H.; McCammon, J. Andrew; Quiocho, Florante A. (J. Am. Chem. Soc., 1990)

The role of hydrogen-bonds in drug binding. - Wade, R. C.; Goodford, P. J. (Prog Clin Biol Res, 1989)
Hydrogen-bonds play a crucial role in determining the specificity of ligand binding. Their important contribution is explicitly incorporated into a computational method, called GRID, which has been designed to detect energetically favourable ligand binding sites on a chosen target molecule of known structure. An empirical energy function consisting of a Lennard-Jones, an electrostatic and a hydrogen-bonding term is employed. The latter term is found to be necessary because spherically symmetric atom-centred forces alone may not adequately reproduce the geometry of two interacting molecules. The hydrogen-bonding term is dependent on the length and orientation of the hydrogen-bond. Its functional form also varies according to the chemical nature of both the hydrogen-bond donor and acceptor atoms, and has been modelled to fit experimental observations of crystal structures. The mobility of the hydrogen-bonding hydrogens is considered analytically in calculating the hydrogen-bond energy. The hydrogen-bonding energy functions will be described and their application will be demonstrated on molecules of pharmacological interest where hydrogen-bonds influence the binding of ligands.
Keywords: Camphor 5-Monooxygenase; Catecholamines/metabolism; Chemical Phenomena; *Chemistry, Physical; Cytochrome P-450 Enzyme System/metabolism; Drug Design; Histidine/metabolism; *Hydrogen Bonding; Ligands; Mathematical Computing; Mixed Function Oxygenases/metabolism; Pharmaceutical Preparations/*metabolism; *Protein Binding; Receptors, Drug/*metabolism; Thermodynamics

New Hydrogen-bond Potentials for Use in Determining Energetically Favourable Binding Sites on Molecules of Known Structure - Boobbyer, David N. A.; Goodford, Peter J.; McWhinnie, Peter M.; Wade, Rebecca C. (J. Med. Chem., 1989)

Identifying Targets for Bioreductive Agents - Reynolds, Christopher A.; Wade, Rebecca C.; Goodford, Peter J. (J. Mol. Graph., 1989)

The Use of Molecular Graphics in the Design of Anti-influenza Agents - Wade, Rebecca C.; Goodford, P.J. (Br. J. Pharmac. Proc. Suppl., 1988)

Ligand-Macromolecule Interactions - Wade, Rebecca C. (1988)

Dynamically adapting the degree of parallelism with reflexive programs - Reimer, Niels; Hänßgen, Stefan U.; Tichy, Walter F. (Parallel Algorithms for Irregularly Structured Problems, 1996)

An Algorithmic Approach to Peptidomimetics - Banerjee, Priyanka (2013)

Dynamische hybride Cloud für wissenschaftliche Anwendungen - Monninger, Thomas (2012)

Sequence, Structure and Stability of Collagen and its Interaction with Collagenase. - Subramaniam, Sundar Raman (2011)

Computational and NMR Studies of Thymidylate Synthase and its Regulation - Garg, Divita (2011)

Structural Comparison of Pyruvate Kinases. - Veith, Nadine (2011)

System Approach to the Identification of Folate-related Enzyme Inhibitors with Anti-infectious Action - Nerini, Erika (2011)

Computation and Modeling of Molecular Recognition: The Cysteine Synthase Complex - Feldman-Salit, Anna (2010)

Linker Histone-Nucleosome Interactions: A Modelling and Simulation Study - Pachov, Georgi V. (2009)

Automatisierte Analyse von Brownian Dynamics Simulationen - Berynskyy, Mykhaylo (2009)

Modeling of macromolecular interactions - Motiejunas, Domantas (2007)

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) - Zahran, Mai (2006)

Development of a software to aid the search of protein structural information to estimate kinetic parameters in systems biology applications - Besson, Bruno (2005)

Protein-protein docking assisted by sequence conservation and experimental data - Motiejunas, Domantas (2004)

Peroxidases: A computational study of ligand binding and enzyme kinetics - R.Hallingbaeck, Henrik (2004)

Using Sequence Information in Protein Docking Procedures - Doudieu, Octave M. Noubibou (2003)

High-throughput Structural and Electrostatic Modelling of Ubiquitin Conjugating Enzymes - Battey, James N.D. (2003)

Structure-based design of inhibitors of enzymes of the ubiquitin mediated protein degradation pathway - Pulagam, Lakshmi V. Padmavathi (2003)

Inhibition studies of enzymes involved in drug resistance phenomena. Library-design and Structure-based approaches towards species-specific inhibitors of Thymidylate Synthase - Ferrari, Stefania (2001)

Molecular Dynamics and NMR Spectroscopic Studies of Local Interactions of Small Peptides in Aqueous Solution Involving Aromatic Residues - Nardi, Frederico (1999)

Computational studies of blue copper proteins - Rienzo, Francesca De (1999)

Chloride ion exchange routes in Haloalkane Dehalogenase from Xanthobacter autrophicus detected by Thermal Motion Pathway analysis, GRID and Essential Dynamics - Koboyashi, Masakazu (1999)

Binding of Glycosaminoglycans to Heparin-Binding Proteins - Bitomsky, Wolfgang (1998)

Rational design of Human Synovial Fluid Phospholipase A2 inhibitors and analysis of their three-dimensional structure-activity relationships - Ortiz, Angel Ramirez (1996)

Hydratation des aktiven Zentrums von Cytochrom P450cam - Untersuchung mit Molekueldynamik-Simulationen - Helms, Volkhard (1996)

Modeling and Simulation of Protein-Surface Interactions - Ozboyaci, Musa (2016)

Development of Hydrodynamic Coarse-Grain Models for Brownian Dynamics Simulations of Crowded Protein Systems - Reinhardt, Martin (2017)

Modeling and Simulation of Membrane Proteins to Understand their Structure, Dynamics and Function - Mustafa, Ghulam (2017)

Computational Studies on the Relation Between Macromolecular Dynamics and Protein Binding and Function. - Stank, Antonia (2017)

A novel method to treat gated protein-ligand binding via on-the-fly conformational updates within rigid body BD simulations - Friedrich, Patrick (2018)

A computational approach to decipher chromatosome structure determinants - Öztuerk, Mehmet Ali (2018)

Macromolecular Interactions: in silico prediction of the structures of complexes between proteins - Berinski, Michael (2015)

Methods to Compute and Investigate Drug Binding Kinetics - Ganotra, Gaurav Kumar (2015)

Multiscale Simulations of Cytochrome P450 Systems - Yu, Xiaofeng (2015)

Positivity and higher Teichmüller theory - Guichard, Olivier; Wienhard, Anna (European Congress of Mathematics, 2018)
We introduce Θ-positivity, a new notion of positivity in real semisimple Lie groups. The notion of Θ-positivity generalizes at the same time Lusztig’s total positivity in split real Lie groups as well as well known concepts of positivity in Lie groups of Hermitian type. We show that there are two other families of Lie groups, \SO(p,q) for p<q, and a family of exceptional Lie groups, which admit a Θ-positive structure. We describe key aspects of Θ-positivity and make a connection with representations of surface groups and higher Teichmüller theory.

Deforming convex real projective structures - Wienhard, Anna; Zhang, Tengren (Geometriae dedicata, 2018)
Let S be a closed, connected, orientable surface of genus at least 2, and let C(S) denote the deformation space of convex real projective structures S. In this article, we introduce two new flows on C(S), which we call the internal bulging flow and the eruption flow. These are geometrically defined flows associated to each pair of pants in a pants decomposition on S that deform the internal parameters. We show that the eruption flows, together with the generalized twist flows about the pants curves, give rise to a half-dimensional family of commuting flows on C(S).

Limits of Geometries - Cooper, Daryl; Danciger, Jeffrey; Wienhard, Anna (Transactions of the American Mathematical Society, 2018)
A geometric transition is a continuous path of geometric structures that changes type, meaning that the model geometry, i.e., the homogeneous space on which the structures are modeled, abruptly changes. In order to rigorously study transitions, one must define a notion of geometric limit at the level of homogeneous spaces, describing the basic process by which one homogeneous geometry may transform into another. We develop a general framework to describe transitions in the context that both geometries involved are represented as sub-geometries of a larger ambient geometry. Specializing to the setting of real projective geometry, we classify the geometric limits of any sub-geometry whose structure group is a symmetric subgroup of the projective general linear group. As an application, we classify all limits of three-dimensional hyperbolic geometry inside of projective geometry, finding Euclidean, Nil, and Sol geometry among the limits. We prove, however, that the other Thurston geometries, in particular \mathbbH^2 × \mathbbR and \widetilde \textup SL_2\mathbbR, do not embed in any limit of hyperbolic geometry in this sense.

Horofunction Compactifications of Symmetric Spaces - Haettel, Thomas; Schilling, Anna; Walsh, Cormac; Wienhard, Anna (arXiV preprints, 2017)
We consider horofunction compactifications of symmetric spaces with respect to invariant Finsler metrics. We show that any (generalized) Satake compactification can be realized as a horofunction compactification with respect to a polyhedral Finsler metric.

On weakly maximal representations of surface groups - Ben Simon, Gabi; Burger, Marc; Hartnick, Tobias; Iozzi, Alessandra; Wienhard, Anna (Journal of differential geometry, 2017)
We introduce and study a new class of representations of surface groups into Lie groups of Hermitian type, called weakly maximal representations. We prove that weakly maximal representations are discrete and injective and we describe the structure of the Zariski closure of their image. Furthermore, we prove that the set of weakly maximal representations is a closed subset of the representation variety and describe its relation to other geometrically significant subsets of the representations variety.

Anosov representations and proper actions - Guéritaud, François; Guichard, Olivier; Kassel, Fanny; Wienhard, Anna (Geometry & Topology, 2017)
We establish several characterizations of Anosov representations of word hyperbolic groups into real reductive Lie groups, in terms of a Cartan projection or Lyapunov projection of the Lie group. Using a properness criterion of Benoist and Kobayashi, we derive applications to proper actions on homogeneous spaces of reductive groups.

On order-preserving representations - Ben Simon, G.; Burger, M.; Hartnick, T.; Iozzi, A.; Wienhard, Anna (Journal of the London Mathematical Society, 2016)
In this article we introduce order preserving representations of fundamental groups of surfaces into Lie groups with bi-invariant orders. By relating order preserving representations to weakly maximal representations, introduced in arXiv:1305.2620, we show that order preserving representations into Lie groups of Hermitian type are faithful with discrete image and that the set of order preserving representations is closed in the representation variety. For Lie groups of Hermitian type whose associated symmetric space is of tube type we give a geometric characterization of these representations in terms of the causal structure on the Shilov boundary.

Integration of internal and external gene expression and drug-perturbation data to empower novel immune therapies against Parkinson’s Disease - Biczok, Rudolf (2019)

Technical and Algorithmic Optimization of PaPaRa - Wegmann, Johanna (2019)

Quantitave Analysis of Phylogenetic Quasi-Terraces - Breitling, Paula (2019)

A review of approaches for optimizing phylogenetic likelihood calculations - Stamatakis, Alexandros (2019)

Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence - Zhou, Xiaofan; Lutteropp, Sarah; Czech, Lucas; Stamatakis, Alexandros; Looz, Moritz Von; Rokas, Antonis (Systematic Biology, 2019)

Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV - Serdari, Dora; Kostaki, Evangelia-Georgia; Paraskevis, Dimitrios; Stamatakis, Alexandros; Kapli, Paschalia (PeerJ, 2019)

An empirical analysis of enzyme function reporting for experimental reproducibility: Missing/incomplete information in published papers - Halling, Peter; Fitzpatrick, Paul F.; Raushel, Frank M.; Rohwer, Johann; Schnell, Santiago; Wittig, Ulrike; Wohlgemuth, Roland; Kettner, Carsten (Biophysical Chemistry, 2018)

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics - Wittig, Ulrike; Rey, Maja; Weidemann, Andreas; Kania, Renate; Müller, Wolfgang (Nucleic Acids Research, 2018)

STRENDA DB: enabling the validation and sharing of enzyme kinetics data - Swainston, Neil; Baici, Antonio; Bakker, Barbara M.; Cornish‐Bowden, Athel; Fitzpatrick, Paul F.; Halling, Peter; Leyh, Thomas S.; O'Donovan, Claire; Raushel, Frank M.; Reschel, Udo; Rohwer, Johann M.; Schnell, Santiago; et al. (The FEBS Journal, 2018)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017 - Schreiber, Falk; Bader, Gary D.; Gleeson, Padraig; Golebiewski, Martin; Hucka, Michael; Keating, Sarah M.; Novère, Nicolas Le; Myers, Chris; Nickerson, David; Sommer, Björn; Waltemath, Dagmar (Journal of Integrative Bioinformatics, 2018)

Graphs of curves on infinite-type surfaces with mapping class group actions - Durham, Matthew Gentry; Fanoni, Federica; Vlamis, Nicholas G. (Annales de l'Institut Fourier, 2018)
We study when the mapping class group of an infinite-type surface S admits an action with unbounded orbits on a connected graph whose vertices are simple closed curves on S. We introduce a topological invariant for infinite-type surfaces that determines in many cases whether there is such an action. This allows us to conclude that, as non-locally compact topological groups, many big mapping class groups have nontrivial coarse geometry in the sense of Rosendal.

Mapping class group orbits of curves with self-intersections - Cahn, Patricia; Fanoni, Federica; Petri, Bram (Israel J. Math., 2018)

A Multi-resolution Approach to the Simulation of Protein Complexes in a Membrane Bilayer - Mukherjee, Goutam; Nandekar, Prajwal; Mustafa, Ghulam; Richter, Stefan; Wade, Rebecca C. (High Performance Computing in Science and Engineering ' 18, 2019)

Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19 - Mustafa, Ghulam; Nandekar, Prajwal P.; Bruce, Neil J.; Wade, Rebecca C. (International Journal of Molecular Sciences, 2019)

Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity - Blomberg, Niklas; Gabdoulline, Razif R.; Nilges, Michael; Wade, Rebecca C. (Proteins: Structure, Function, and Genetics, 1999)

On the protein-protein diffusional encounter complex - Gabdoulline, Razif R.; Wade, Rebecca C. (Journal of Molecular Recognition, 1999)

Hydration energy landscape of the active site cavity in cytochrome P450cam - Helms, Volkhard; Wade, Rebecca C. (Proteins: Structure, Function, and Genetics, 1998)

Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases - Wade, Rebecca C.; Gabdoulline, Razif R.; Luty, Brock A. (Proteins: Structure, Function, and Genetics, 1998)

Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy - Helms, Volkhard; Wade, Rebecca C. (Journal of Computational Chemistry, 1997)

StarDOM: From STAR format to XML - Linge, Jens P.; Nilges, Michael; Ehrlich, Lutz (Journal of Biomolecular NMR, 1999)

Comparative binding energy analysis - Wade, Rebecca C.; Ortiz, Angel R.; Gago, Federico (Perspectives in Drug Discovery and Design, 1998)

Higgs bundles for real groups and the Hitchin-Kostant-Rallis section - García-Prada, Oscar; Peón-Nieto, Ana; Ramanan, S. (Transactions of the American Mathematical Society, 2018)
We consider the moduli space of polystable-twisted-Higgs bundles over a compact Riemann surface, where is a real reductive Lie group and is a holomorphic line bundle over. Evaluating the Higgs field on a basis of the ring of polynomial invariants of the isotropy representation defines the Hitchin map.

Cameral data for SU(p+1,p)-Higgs bundles - Peón-Nieto, Ana (arXiV preprints, 2015)
We study the cameral and spectral data for the moduli space of polystable \SU(p+1,p)-Higgs bundles and deduce the latter from the former. As an application, we obtain that the Toledo invariant classifies the connected components of the regular fibers of the Hitchin map.

Using RAxML-NG in Practice - Kozlov, Alexey; Stamatakis, Alexandros (2019)

Milnor-Wood type inequalities for Higgs bundles - Hartnick, Tobias; Ott, Andreas (arXiV preprints, 2011)
We explain how the generalized Milnor–Wood inequality of Burger and Iozzi for reductive representations of a cocompact complex-hyperbolic lattice into a Hermitian Lie group translates under the non-abelian Hodge correspondence into an inequality for topological invariants of the corresponding Higgs bundles. In this manner, we obtain in a uniform way a universal Milnor–Wood inequality for Higgs bundles over complex-hyperbolic manifolds of arbitrary dimensions and with arbitrary Hermitian structure group. This complements results of Biquard, Bradlow, García-Prada, Gothen, Mundet, Rubio and Chaput, Koziarz, Maubon.

Perturbations of the Spence-Abel equation and deformations of the dilogarithm function - Hartnick, Tobias; Ott, Andreas (Mathematische Annalen, 2017)
We analyze existence, uniqueness and regularity of solutions for perturbations of the Spence-Abel equation for the Rogers’ dilogarithm. As an application we deduce a version of Hyers-Ulam stability for the Spence-Abel equation.

Bounded cohomology via partial differential equations, I - Hartnick, Tobias; Ott, Andreas (Geometry and Topology, 2015)
We present a new technique that employs partial differential equations in order to explicitly construct primitives in the continuous bounded cohomology of Lie groups. As anapplication, we prove a vanishing theorem for the continuous bounded cohomology of SL(2,R) in degree four, establishing a special case of a conjecture of Monod.

Transgression in bounded cohomology and a conjecture of Monod - Ott, Andreas (Journal of Topology and Analysis, 2019)
We develop an algebro-analytic framework for the systematic study of the con-tinuous bounded cohomology of Lie groups in large degree. As an application, we examine the continuous bounded cohomology of \mathrmPSL(2,\mathbb R) with trivial real coefficients in all degrees greater than two. We prove a vanishing result for strongly reducible classes, thus providing further evidence for a conjecture of Monod. On the cochain level, our method yields explicit formulas for cohomological primitives of arbitrary bounded cocycles.

Geometry of compact complex manifolds associated to generalized quasi-Fuchsian representations - Dumas, David; Sanders, Andy ((to be published in Geometry and Topology), 2017)
We study the topology and geometry of compact complex manifolds associated to Anosov representations of surface groups and other hyperbolic groups in a complex semisimple Lie group G. These manifolds are obtained as quotients of the domains of discontinuity in generalized flag varieties G/P constructed by Kapovich-Leeb-Porti (arXiv:1306.3837), and in some cases by Guichard-Wienhard (arXiv:1108.0733). For G-Fuchsian representations and their Anosov deformations, where G is simple, we compute the homology of the domains of discontinuity and of the quotient manifolds. For G-Fuchsian and G-quasi-Fuchsian representations in simple G of rank at least two, we show that the quotient manifolds are not Kähler. We also describe the Picard groups of these quotient manifolds, compute the cohomology of line bundles on them, and show that for G of sufficiently large rank these manifolds admit nonconstant meromorphic functions. In a final section, we apply our topological results to several explicit families of domains and derive closed formulas for topological invariants in some cases. We also show that the quotient manifold for a G-Fuchsian representation in \mathrmPSL_3(C) is a fiber bundle over a surface, and we conjecture that this holds for all simple G.

(G,P)-opers and global Slodowy slices - Collier, Brian; Sanders, Andy (arXiv,math.DG,1911.12844, 2019)
In this paper, we introduce a generalization of G-opers for arbitrary parabolic subgroups P<G. For parabolic subgroups associated to even nilpotents, we parameterize (G,P)-opers by an object generalizing the base of the Hitchin fibration. In particular, we describe families of opers associated to higher Teichmuller spaces

Domains of discontinuity for almost-Fuchsian groups - Sanders, Andy (Transactions of the American Mathematical Society, 2017)
An almost-Fuchsian group is a quasi-Fuchsian group such that the quotient hyperbolic manifold contains a closed incompressible minimal surface with principal curvatures contained in (-1,1) . We show that the domain of discontinuity of an almost-Fuchsian group contains many balls of a fixed spherical radius in the visual boundary of hyperbolic 3-space. This yields a necessary condition for a quasi-Fuchsian group to be almost-Fuchsian which involves only conformal geometry. As an application, we prove that there are no doubly-degenerate geometric limits of almost-Fuchsian groups.