Holger Gohlke

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 19

Top Topics

Influenza Virus

Protein Structure

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

PLoS Comput. Biol.

Publications

David A. Case, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet Cagri Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R. Machado, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason M. Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
AmberTools. J. Chem. Inf. Model. 63 (20) (2023)
Fathoni A. Musyaffa, Kirsten Rapp, Holger Gohlke
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW. J. Chem. Inf. Model. 63 (20) (2023)
Till El Harrar, Holger Gohlke
Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J. Chem. Inf. Model. 63 (1) (2023)
Karel J. van der Weg, Holger Gohlke
TopEnzyme: a framework and database for structural coverage of the functional enzyme space. Bioinform. 39 (3) (2023)
Christina Nutschel, Cristina Coscolín, Benoit David, Daniel Mulnaes, Manuel Ferrer, Karl-Erich Jaeger, Holger Gohlke
Promiscuous Esterases Counterintuitively Are Less Flexible than Specific Ones. J. Chem. Inf. Model. 61 (5) (2021)
Daniel Mulnaes, Filip Koenig, Holger Gohlke
TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction. J. Chem. Inf. Model. 61 (2) (2021)
Daniel Becker, Prasad V. Bharatam, Holger Gohlke
F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism. J. Chem. Inf. Model. 61 (8) (2021)
Sabahuddin Ahmad, Christoph Heinrich Strunk, Stephan Schott-Verdugo, Karl-Erich Jaeger, Filip Kovacic, Holger Gohlke
Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity. J. Chem. Inf. Model. 61 (11) (2021)
Lucas Wäschenbach, Christoph G. W. Gertzen, Verena Keitel, Holger Gohlke
Dimerization energetics of the G-protein coupled bile acid receptor TGR5 from all-atom simulations. J. Comput. Chem. 41 (9) (2020)
Neha Verma, Peter Dollinger, Filip Kovacic, Karl-Erich Jaeger, Holger Gohlke
The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A. J. Comput. Chem. 41 (6) (2020)
Christina Nutschel, Alexander Fulton, Olav Zimmermann, Ulrich Schwaneberg, Karl-Erich Jaeger, Holger Gohlke
Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A. J. Chem. Inf. Model. 60 (3) (2020)
Jonas Dittrich, Denis Schmidt, Christopher Pfleger, Holger Gohlke
Converging a Knowledge-Based Scoring Function: DrugScore2018. J. Chem. Inf. Model. 59 (1) (2019)
Stephan Schott-Verdugo, Holger Gohlke
PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building. J. Chem. Inf. Model. 59 (6) (2019)
Christian A. Hanke, Holger Gohlke
Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site. J. Chem. Inf. Model. 57 (11) (2017)
Ido Y. Ben-Shalom, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke
Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations. J. Chem. Inf. Model. 57 (2) (2017)
Benedikt Frieg, Boris Görg, Nadine Homeyer, Verena Keitel, Dieter Häussinger, Holger Gohlke
Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies. PLoS Comput. Biol. 12 (2) (2016)
Harris Ioannidis, Antonios Drakopoulos, Christina Tzitzoglaki, Nadine Homeyer, Felix Kolarov, Paraskevi Gkeka, Kathrin Freudenberger, Christos Liolios, Günter Gauglitz, Zoe Cournia, Holger Gohlke, Antonios Kolocouris
Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM. J. Chem. Inf. Model. 56 (5) (2016)
Nadine Homeyer, Harris Ioannidis, Felix Kolarov, Günter Gauglitz, Christos Zikos, Antonios Kolocouris, Holger Gohlke
Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations. J. Chem. Inf. Model. 56 (1) (2016)
Prakash Chandra Rathi, Alexander Fulton, Karl-Erich Jaeger, Holger Gohlke
. PLoS Comput. Biol. 12 (3) (2016)
Prakash Chandra Rathi, Daniel Mulnaes, Holger Gohlke
VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability. Bioinform. 31 (14) (2015)
Prakash Chandra Rathi, Hans Wolfgang Höffken, Holger Gohlke
Quality Matters: Extension of Clusters of Residues with Good Hydrophobic Contacts Stabilize (Hyper)Thermophilic Proteins. J. Chem. Inf. Model. 54 (2) (2014)
Alexander Metz, Julia Schanda, Manuel Grez, Christian Wichmann, Holger Gohlke
From Determinants of RUNX1/ETO Tetramerization to Small-Molecule Protein-Protein Interaction Inhibitors Targeting Acute Myeloid Leukemia. J. Chem. Inf. Model. 53 (9) (2013)
Christopher Pfleger, Prakash Chandra Rathi, Doris L. Klein, Sebastian Radestock, Holger Gohlke
Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function. J. Chem. Inf. Model. 53 (4) (2013)
Holger Gohlke, Ulrike Hergert, Tatu Meyer, Daniel Mulnaes, Manfred K. Grieshaber, Sander H. J. Smits, Lutz Schmitt
Binding Region of Alanopine Dehydrogenase Predicted by Unbiased Molecular Dynamics Simulations of Ligand Diffusion. J. Chem. Inf. Model. 53 (10) (2013)
Nadine Homeyer, Holger Gohlke
FEW: A workflow tool for free energy calculations of ligand binding. J. Comput. Chem. 34 (11) (2013)
Dennis M. Krüger, Prakash Chandra Rathi, Christopher Pfleger, Holger Gohlke
CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Christopher Pfleger, Sebastian Radestock, Elena Schmidt, Holger Gohlke
Global and local indices for characterizing biomolecular flexibility and rigidity. J. Comput. Chem. 34 (3) (2013)
Alexander Metz, Christopher Pfleger, Hannes Kopitz, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke
Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein-Protein Interface. J. Chem. Inf. Model. 52 (1) (2012)
Hannes Kopitz, Daniel A. Cashman, Stefania Pfeiffer-Marek, Holger Gohlke
Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance-dependent dielectric model. J. Comput. Chem. 33 (9) (2012)
Dennis M. Krüger, Gisela Jessen, Holger Gohlke
How Good Are State-of-the-Art Docking Tools in Predicting Ligand Binding Modes in Protein-Protein Interfaces? J. Chem. Inf. Model. 52 (11) (2012)
Sandra Dreisigacker, Dorota Latek, Svenja Bockelmann, Markus Huss, Helmut Wieczorek, Slawomir Filipek, Holger Gohlke, Dirk Menche, Teresa Carlomagno
Understanding the Inhibitory Effect of Highly Potent and Selective Archazolides Binding to the Vacuolar ATPase. J. Chem. Inf. Model. 52 (8) (2012)
Britta Nisius, Sha Fan, Holger Gohlke
Novel binding pocket descriptors based on DrugScore potential fields encoded by 3D Zernike descriptors. J. Cheminformatics 4 (S-1) (2012)
Britta Nisius, Holger Gohlke
Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors. J. Chem. Inf. Model. 52 (9) (2012)
Dennis M. Krüger, Aqeel Ahmed, Holger Gohlke
NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Simone Fulle, Holger Gohlke
Constraint counting on RNA and ribosomal structures: linking flexibility and function. J. Cheminformatics 3 (S-1) (2011)
Holger Gohlke, Alexander Metz, Christopher Pfleger, Dennis M. Krüger, Sina Kazemi
Towards targeting protein-protein interfaces with small molecules. J. Cheminformatics 3 (S-1) (2011)
Aqeel Ahmed, Friedrich Rippmann, Gerhard Barnickel, Holger Gohlke
A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins. J. Chem. Inf. Model. 51 (7) (2011)
Ian R. Craig, Christopher Pfleger, Holger Gohlke, Jonathan W. Essex, Katrin Spiegel
Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins. J. Chem. Inf. Model. 51 (10) (2011)
Dennis M. Krüger, José Ignacio Garzón, P. C. Montes, Holger Gohlke
: fully-flexible docking, scoring, and in silico alanine-scanning. J. Cheminformatics 3 (S-1) (2011)
Simone Fulle, Nina Alexandra Christ, Eva Kestner, Holger Gohlke
HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations. J. Chem. Inf. Model. 50 (8) (2010)
Dennis M. Krüger, Holger Gohlke
alanine scanning for scoring protein-protein interactions. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Dennis M. Krüger, Holger Gohlke
DrugScorePPI for scoring protein-protein interactions: improving a knowledge-based scoring function by atomtype-based QSAR. J. Cheminformatics 2 (S-1) (2010)
Domingo González-Ruiz, Holger Gohlke
Steering Protein-Ligand Docking with Quantitative NMR Chemical Shift Perturbations. J. Chem. Inf. Model. 49 (10) (2009)
Benjamin Breu, Katrin Silber, Holger Gohlke
Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions. J. Chem. Inf. Model. 47 (6) (2007)
Patrick Pfeffer, Holger Gohlke
Knowledge-Based Scoring Function To Predict RNA-Ligand Interactions. J. Chem. Inf. Model. 47 (5) (2007)
David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods
The Amber biomolecular simulation programs. J. Comput. Chem. 26 (16) (2005)
Holger Gohlke, David A. Case
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J. Comput. Chem. 25 (2) (2004)