Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. - Holger Gohlke; David A. Case (J. Comput. Chem., 2004)

The Amber biomolecular simulation programs. - David A. Case; Thomas E. Cheatham III; Tom Darden; Holger Gohlke; Ray Luo 001; Kenneth M. Merz Jr.; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J. Woods (J. Comput. Chem., 2005)

Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions. - Benjamin Breu; Katrin Silber; Holger Gohlke (J. Chem. Inf. Model., 2007)

DrugScoreRNAKnowledge-Based Scoring Function To Predict RNA-Ligand Interactions. - Patrick Pfeffer; Holger Gohlke (J. Chem. Inf. Model., 2007)

Steering Protein-Ligand Docking with Quantitative NMR Chemical Shift Perturbations. - Domingo González-Ruiz; Holger Gohlke (J. Chem. Inf. Model., 2009)

DrugScorePPI for scoring protein-protein interactions: improving a knowledge-based scoring function by atomtype-based QSAR. - Dennis M. Krüger; Holger Gohlke (J. Cheminformatics, 2010)

HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations. - Simone Fulle; Nina Alexandra Christ; Eva Kestner; Holger Gohlke (J. Chem. Inf. Model., 2010)

DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. - Dennis M. Krüger; Holger Gohlke (Nucleic Acids Res., 2010)

Constraint counting on RNA and ribosomal structures: linking flexibility and function. - Simone Fulle; Holger Gohlke (J. Cheminformatics, 2011)

Towards targeting protein-protein interfaces with small molecules. - Holger Gohlke; Alexander Metz; Christopher Pfleger; Dennis M. Krüger; Sina Kazemi (J. Cheminformatics, 2011)

Predicting protein-protein interactions with DrugScorePPI: fully-flexible docking, scoring, and in silico alanine-scanning. - Dennis M. Krüger; José Ignacio Garzón; P. C. Montes; Holger Gohlke (J. Cheminformatics, 2011)

A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins. - Aqeel Ahmed; Friedrich Rippmann; Gerhard Barnickel; Holger Gohlke (J. Chem. Inf. Model., 2011)

Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins. - Ian R. Craig; Christopher Pfleger; Holger Gohlke; Jonathan W. Essex; Katrin Spiegel (J. Chem. Inf. Model., 2011)

Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance-dependent dielectric model. - Hannes Kopitz; Daniel A. Cashman; Stefania Pfeiffer-Marek; Holger Gohlke (J. Comput. Chem., 2012)

Novel binding pocket descriptors based on DrugScore potential fields encoded by 3D Zernike descriptors. - Britta Nisius; Sha Fan; Holger Gohlke (J. Cheminformatics, 2012)

Understanding the Inhibitory Effect of Highly Potent and Selective Archazolides Binding to the Vacuolar ATPase. - Sandra Dreisigacker; Dorota Latek; Svenja Bockelmann; Markus Huss; Helmut Wieczorek; Slawomir Filipek; Holger Gohlke; Dirk Menche; Teresa Carlomagno (J. Chem. Inf. Model., 2012)

How Good Are State-of-the-Art Docking Tools in Predicting Ligand Binding Modes in Protein-Protein Interfaces? - Dennis M. Krüger; Gisela Jessen; Holger Gohlke (J. Chem. Inf. Model., 2012)

Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein-Protein Interface. - Alexander Metz; Christopher Pfleger; Hannes Kopitz; Stefania Pfeiffer-Marek; Karl-Heinz Baringhaus; Holger Gohlke (J. Chem. Inf. Model., 2012)

Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors. - Britta Nisius; Holger Gohlke (J. Chem. Inf. Model., 2012)

NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins. - Dennis M. Krüger; Aqeel Ahmed; Holger Gohlke (Nucleic Acids Res., 2012)

FEW: A workflow tool for free energy calculations of ligand binding. - Nadine Homeyer; Holger Gohlke (J. Comput. Chem., 2013)

Global and local indices for characterizing biomolecular flexibility and rigidity. - Christopher Pfleger; Sebastian Radestock; Elena Schmidt; Holger Gohlke (J. Comput. Chem., 2013)

Binding Region of Alanopine Dehydrogenase Predicted by Unbiased Molecular Dynamics Simulations of Ligand Diffusion. - Holger Gohlke; Ulrike Hergert; Tatu Meyer; Daniel Mulnaes; Manfred K. Grieshaber; Sander H. J. Smits; Lutz Schmitt (J. Chem. Inf. Model., 2013)

From Determinants of RUNX1/ETO Tetramerization to Small-Molecule Protein-Protein Interaction Inhibitors Targeting Acute Myeloid Leukemia. - Alexander Metz; Julia Schanda; Manuel Grez; Christian Wichmann; Holger Gohlke (J. Chem. Inf. Model., 2013)

Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function. - Christopher Pfleger; Prakash Chandra Rathi; Doris L. Klein; Sebastian Radestock; Holger Gohlke (J. Chem. Inf. Model., 2013)

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function. - Dennis M. Krüger; Prakash Chandra Rathi; Christopher Pfleger; Holger Gohlke (Nucleic Acids Res., 2013)

Quality Matters: Extension of Clusters of Residues with Good Hydrophobic Contacts Stabilize (Hyper)Thermophilic Proteins. - Prakash Chandra Rathi; Hans Wolfgang Höffken; Holger Gohlke (J. Chem. Inf. Model., 2014)

VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability. - Prakash Chandra Rathi; Daniel Mulnaes; Holger Gohlke (Bioinform., 2015)

Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations. - Nadine Homeyer; Harris Ioannidis; Felix Kolarov; Günter Gauglitz; Christos Zikos; Antonios Kolocouris; Holger Gohlke (J. Chem. Inf. Model., 2016)

Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM. - Harris Ioannidis; Antonios Drakopoulos; Christina Tzitzoglaki; Nadine Homeyer; Felix Kolarov; Paraskevi Gkeka; Kathrin Freudenberger; Christos Liolios; Günter Gauglitz; Zoe Cournia; Holger Gohlke; Antonios Kolocouris (J. Chem. Inf. Model., 2016)

Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies. - Benedikt Frieg; Boris Görg; Nadine Homeyer; Verena Keitel; Dieter Häussinger; Holger Gohlke (PLoS Comput. Biol., 2016)

Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis. - Prakash Chandra Rathi; Alexander Fulton; Karl-Erich Jaeger; Holger Gohlke (PLoS Comput. Biol., 2016)

Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations. - Ido Y. Ben-Shalom; Stefania Pfeiffer-Marek; Karl-Heinz Baringhaus; Holger Gohlke (J. Chem. Inf. Model., 2017)

Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site. - Christian A. Hanke; Holger Gohlke (J. Chem. Inf. Model., 2017)

Converging a Knowledge-Based Scoring Function: DrugScore2018. - Jonas Dittrich; Denis Schmidt; Christopher Pfleger; Holger Gohlke (J. Chem. Inf. Model., 2019)

PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building. - Stephan Schott-Verdugo; Holger Gohlke (J. Chem. Inf. Model., 2019)

The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A. - Neha Verma 002; Peter Dollinger; Filip Kovacic; Karl-Erich Jaeger; Holger Gohlke (J. Comput. Chem., 2020)

Dimerization energetics of the G-protein coupled bile acid receptor TGR5 from all-atom simulations. - Lucas Wäschenbach; Christoph G. W. Gertzen; Verena Keitel; Holger Gohlke (J. Comput. Chem., 2020)

Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A. - Christina Nutschel; Alexander Fulton; Olav Zimmermann; Ulrich Schwaneberg; Karl-Erich Jaeger; Holger Gohlke (J. Chem. Inf. Model., 2020)

Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity. - Sabahuddin Ahmad; Christoph Heinrich Strunk; Stephan Schott-Verdugo; Karl-Erich Jaeger; Filip Kovacic; Holger Gohlke (J. Chem. Inf. Model., 2021)

F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism. - Daniel Becker 009; Prasad V. Bharatam; Holger Gohlke (J. Chem. Inf. Model., 2021)

TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction. - Daniel Mulnaes; Filip Koenig; Holger Gohlke (J. Chem. Inf. Model., 2021)

Promiscuous Esterases Counterintuitively Are Less Flexible than Specific Ones. - Christina Nutschel; Cristina Coscolín; Benoit David; Daniel Mulnaes; Manuel Ferrer; Karl-Erich Jaeger; Holger Gohlke (J. Chem. Inf. Model., 2021)

Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. - Till El Harrar; Holger Gohlke (J. Chem. Inf. Model., 2023)

TopEnzyme: a framework and database for structural coverage of the functional enzyme space. - Karel J. van der Weg; Holger Gohlke (Bioinform., 2023)

AmberTools. - 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; et al. (J. Chem. Inf. Model., 2023)

LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW. - Fathoni A. Musyaffa; Kirsten Rapp; Holger Gohlke (J. Chem. Inf. Model., 2023)

OneProt: Towards Multi-Modal Protein Foundation Models. - 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 (CoRR, 2024)

Molecular Mechanisms Underlying Single Nucleotide Polymorphism-Induced Reactivity Decrease in CYP2D6. - Daniel Becker 009; Prasad V. Bharatam; Holger Gohlke (J. Chem. Inf. Model., 2024)

PyPE_RESP: A Tool to Facilitate and Standardize Derivation of RESP Charges. - Marco Lapsien; Michele Bonus; Lianne Gahan; Adélaïde Raguin; Holger Gohlke (J. Chem. Inf. Model., 2025)