Holger Gohlke - RankMe

52 papers Journal 52

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Evidence for Epibatidine Binding to the Desensitization Gate in α7 nAChR from Molecular Dynamics Simulations and Cryo-EM. J. Chem. Inf. Model. Jesko Kaiser, Christoph G. W. Gertzen, Daniel Mann, Carsten Sachse, Holger Gohlke
2025	J	`jnl`	OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders. PLoS Comput. Biol. Klemens Flöge, Srisruthi Udayakumar, Johanna Sommer, Marie Piraud, Stefan Kesselheim, Vincent Fortuin, Stephan Günnemann, Karel J. van der Weg, Holger Gohlke, Erinc Merdivan, Alina Bazarova
2025	J	`jnl`	PyPE_RESP: A Tool to Facilitate and Standardize Derivation of RESP Charges. J. Chem. Inf. Model. Marco Lapsien, Michele Bonus, Lianne Gahan, Adélaïde Raguin, Holger Gohlke
2024	J	`jnl`	Molecular Mechanisms Underlying Single Nucleotide Polymorphism-Induced Reactivity Decrease in CYP2D6. J. Chem. Inf. Model. Daniel Becker, Prasad V. Bharatam, Holger Gohlke
2024	J	`jnl`	OneProt: Towards Multi-Modal Protein Foundation Models. CoRR Klemens Flöge, Srisruthi Udayakumar, Johanna Sommer, Marie Piraud, Stefan Kesselheim, Vincent Fortuin, Stephan Günnemann, Karel J. van der Weg, Holger Gohlke, Alina Bazarova, Erinc Merdivan
2023	J	`jnl`	AmberTools. J. Chem. Inf. Model. 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.
2023	J	`jnl`	Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J. Chem. Inf. Model. Till El Harrar, Holger Gohlke
2023	J	`jnl`	LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW. J. Chem. Inf. Model. Fathoni A. Musyaffa, Kirsten Rapp, Holger Gohlke
2023	J	`jnl`	TopEnzyme: a framework and database for structural coverage of the functional enzyme space. Bioinform. Karel J. van der Weg, Holger Gohlke
2021	J	`jnl`	F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism. J. Chem. Inf. Model. Daniel Becker, Prasad V. Bharatam, Holger Gohlke
2021	J	`jnl`	Promiscuous Esterases Counterintuitively Are Less Flexible than Specific Ones. J. Chem. Inf. Model. Christina Nutschel, Cristina Coscolín, Benoit David, Daniel Mulnaes, Manuel Ferrer, Karl-Erich Jaeger, Holger Gohlke
2021	J	`jnl`	Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity. J. Chem. Inf. Model. Sabahuddin Ahmad, Christoph Heinrich Strunk, Stephan Schott-Verdugo, Karl-Erich Jaeger, Filip Kovacic, Holger Gohlke
2021	J	`jnl`	TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction. J. Chem. Inf. Model. Daniel Mulnaes, Filip Koenig, Holger Gohlke
2020	J	`jnl`	Dimerization energetics of the G-protein coupled bile acid receptor TGR5 from all-atom simulations. J. Comput. Chem. Lucas Wäschenbach, Christoph G. W. Gertzen, Verena Keitel, Holger Gohlke
2020	J	`jnl`	Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A. J. Chem. Inf. Model. Christina Nutschel, Alexander Fulton, Olav Zimmermann, Ulrich Schwaneberg, Karl-Erich Jaeger, Holger Gohlke
2020	J	`jnl`	The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A. J. Comput. Chem. Neha Verma, Peter Dollinger, Filip Kovacic, Karl-Erich Jaeger, Holger Gohlke
2019	J	`jnl`	Converging a Knowledge-Based Scoring Function: DrugScore2018. J. Chem. Inf. Model. Jonas Dittrich, Denis Schmidt, Christopher Pfleger, Holger Gohlke
2019	J	`jnl`	PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building. J. Chem. Inf. Model. Stephan Schott-Verdugo, Holger Gohlke
2017	J	`jnl`	Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations. J. Chem. Inf. Model. Ido Y. Ben-Shalom, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke
2017	J	`jnl`	Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site. J. Chem. Inf. Model. Christian A. Hanke, Holger Gohlke
2016	J	`jnl`	Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM. J. Chem. Inf. Model. Harris Ioannidis, Antonios Drakopoulos, Christina Tzitzoglaki, Nadine Homeyer, Felix Kolarov, Paraskevi Gkeka, Kathrin Freudenberger, Christos Liolios, Günter Gauglitz, Zoe Cournia, Holger Gohlke, Antonios Kolocouris
2016	J	`jnl`	Application of Rigidity Theory to the Thermostabilization of Lipase A from PLoS Comput. Biol. Prakash Chandra Rathi, Alexander Fulton, Karl-Erich Jaeger, Holger Gohlke
2016	J	`jnl`	Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations. J. Chem. Inf. Model. Nadine Homeyer, Harris Ioannidis, Felix Kolarov, Günter Gauglitz, Christos Zikos, Antonios Kolocouris, Holger Gohlke
2016	J	`jnl`	Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies. PLoS Comput. Biol. Benedikt Frieg, Boris Görg, Nadine Homeyer, Verena Keitel, Dieter Häussinger, Holger Gohlke
2015	J	`jnl`	VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability. Bioinform. Prakash Chandra Rathi, Daniel Mulnaes, Holger Gohlke
2014	J	`jnl`	Quality Matters: Extension of Clusters of Residues with Good Hydrophobic Contacts Stabilize (Hyper)Thermophilic Proteins. J. Chem. Inf. Model. Prakash Chandra Rathi, Hans Wolfgang Höffken, Holger Gohlke
2013	J	`jnl`	Binding Region of Alanopine Dehydrogenase Predicted by Unbiased Molecular Dynamics Simulations of Ligand Diffusion. J. Chem. Inf. Model. Holger Gohlke, Ulrike Hergert, Tatu Meyer, Daniel Mulnaes, Manfred K. Grieshaber, Sander H. J. Smits, Lutz Schmitt
2013	J	`jnl`	CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function. Nucleic Acids Res. Dennis M. Krüger, Prakash Chandra Rathi, Christopher Pfleger, Holger Gohlke
2013	J	`jnl`	Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function. J. Chem. Inf. Model. Christopher Pfleger, Prakash Chandra Rathi, Doris L. Klein, Sebastian Radestock, Holger Gohlke
2013	J	`jnl`	FEW: A workflow tool for free energy calculations of ligand binding. J. Comput. Chem. Nadine Homeyer, Holger Gohlke
2013	J	`jnl`	From Determinants of RUNX1/ETO Tetramerization to Small-Molecule Protein-Protein Interaction Inhibitors Targeting Acute Myeloid Leukemia. J. Chem. Inf. Model. Alexander Metz, Julia Schanda, Manuel Grez, Christian Wichmann, Holger Gohlke
2013	J	`jnl`	Global and local indices for characterizing biomolecular flexibility and rigidity. J. Comput. Chem. Christopher Pfleger, Sebastian Radestock, Elena Schmidt, Holger Gohlke
2012	J	`jnl`	Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors. J. Chem. Inf. Model. Britta Nisius, Holger Gohlke
2012	J	`jnl`	Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein-Protein Interface. J. Chem. Inf. Model. Alexander Metz, Christopher Pfleger, Hannes Kopitz, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke
2012	J	`jnl`	How Good Are State-of-the-Art Docking Tools in Predicting Ligand Binding Modes in Protein-Protein Interfaces? J. Chem. Inf. Model. Dennis M. Krüger, Gisela Jessen, Holger Gohlke
2012	J	`jnl`	Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance-dependent dielectric model. J. Comput. Chem. Hannes Kopitz, Daniel A. Cashman, Stefania Pfeiffer-Marek, Holger Gohlke
2012	J	`jnl`	NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins. Nucleic Acids Res. Dennis M. Krüger, Aqeel Ahmed, Holger Gohlke
2012	J	`jnl`	Novel binding pocket descriptors based on DrugScore potential fields encoded by 3D Zernike descriptors. J. Cheminformatics Britta Nisius, Sha Fan, Holger Gohlke
2012	J	`jnl`	Understanding the Inhibitory Effect of Highly Potent and Selective Archazolides Binding to the Vacuolar ATPase. J. Chem. Inf. Model. Sandra Dreisigacker, Dorota Latek, Svenja Bockelmann, Markus Huss, Helmut Wieczorek, Slawomir Filipek, Holger Gohlke, Dirk Menche, Teresa Carlomagno
2011	J	`jnl`	A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins. J. Chem. Inf. Model. Aqeel Ahmed, Friedrich Rippmann, Gerhard Barnickel, Holger Gohlke
2011	J	`jnl`	Constraint counting on RNA and ribosomal structures: linking flexibility and function. J. Cheminformatics Simone Fulle, Holger Gohlke
2011	J	`jnl`	Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins. J. Chem. Inf. Model. Ian R. Craig, Christopher Pfleger, Holger Gohlke, Jonathan W. Essex, Katrin Spiegel
2011	J	`jnl`	Predicting protein-protein interactions with DrugScore J. Cheminformatics Dennis M. Krüger, José Ignacio Garzón, P. C. Montes, Holger Gohlke
2011	J	`jnl`	Towards targeting protein-protein interfaces with small molecules. J. Cheminformatics Holger Gohlke, Alexander Metz, Christopher Pfleger, Dennis M. Krüger, Sina Kazemi
2010	J	`jnl`	DrugScore Nucleic Acids Res. Dennis M. Krüger, Holger Gohlke
2010	J	`jnl`	DrugScorePPI for scoring protein-protein interactions: improving a knowledge-based scoring function by atomtype-based QSAR. J. Cheminformatics Dennis M. Krüger, Holger Gohlke
2010	J	`jnl`	HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations. J. Chem. Inf. Model. Simone Fulle, Nina Alexandra Christ, Eva Kestner, Holger Gohlke
2009	J	`jnl`	Steering Protein-Ligand Docking with Quantitative NMR Chemical Shift Perturbations. J. Chem. Inf. Model. Domingo González-Ruiz, Holger Gohlke
2007	J	`jnl`	Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions. J. Chem. Inf. Model. Benjamin Breu, Katrin Silber, Holger Gohlke
2007	J	`jnl`	DrugScore J. Chem. Inf. Model. Patrick Pfeffer, Holger Gohlke
2005	J	`jnl`	The Amber biomolecular simulation programs. J. Comput. Chem. 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
2004	J	`jnl`	Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J. Comput. Chem. Holger Gohlke, David A. Case