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Holger Gohlke
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2020 – today
- 2023
- [j47]Karel J. van der Weg
, Holger Gohlke:
TopEnzyme: a framework and database for structural coverage of the functional enzyme space. Bioinform. 39(3) (2023) - [j46]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): 281-298 (2023) - [j45]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): 6183-6191 (2023) - [j44]Fathoni A. Musyaffa, Kirsten Rapp, Holger Gohlke
:
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW. J. Chem. Inf. Model. 63(20): 6224-6238 (2023) - 2021
- [j43]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): 548-553 (2021) - [j42]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): 2383-2395 (2021) - [j41]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): 4023-4030 (2021) - [j40]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): 5626-5643 (2021) - 2020
- [j39]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): 500-512 (2020) - [j38]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): 874-884 (2020) - [j37]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): 1568-1584 (2020)
2010 – 2019
- 2019
- [j36]Jonas Dittrich
, Denis Schmidt
, Christopher Pfleger, Holger Gohlke
:
Converging a Knowledge-Based Scoring Function: DrugScore2018. J. Chem. Inf. Model. 59(1): 509-521 (2019) - [j35]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): 2522-2528 (2019) - 2017
- [j34]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): 170-189 (2017) - [j33]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): 2822-2832 (2017) - 2016
- [j32]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): 110-126 (2016) - [j31]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): 862-876 (2016) - [j30]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) - [j29]Prakash Chandra Rathi
, Alexander Fulton, Karl-Erich Jaeger, Holger Gohlke:
Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis. PLoS Comput. Biol. 12(3) (2016) - 2015
- [j28]Prakash Chandra Rathi
, Daniel Mulnaes, Holger Gohlke:
VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability. Bioinform. 31(14): 2394-2396 (2015) - 2014
- [j27]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): 355-361 (2014) - 2013
- [j26]Christopher Pfleger, Sebastian Radestock, Elena Schmidt, Holger Gohlke:
Global and local indices for characterizing biomolecular flexibility and rigidity. J. Comput. Chem. 34(3): 220-233 (2013) - [j25]Nadine Homeyer, Holger Gohlke:
FEW: A workflow tool for free energy calculations of ligand binding. J. Comput. Chem. 34(11): 965-973 (2013) - [j24]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): 1007-1015 (2013) - [j23]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): 2197-2202 (2013) - [j22]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): 2493-2498 (2013) - [j21]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): 340-348 (2013) - 2012
- [j20]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): 1004-1013 (2012) - [j19]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): 28 (2012) - [j18]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): 120-133 (2012) - [j17]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): 2265-2272 (2012) - [j16]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): 2339-2347 (2012) - [j15]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): 2807-2811 (2012) - [j14]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): 310-316 (2012) - 2011
- [j13]Simone Fulle, Holger Gohlke:
Constraint counting on RNA and ribosomal structures: linking flexibility and function. J. Cheminformatics 3(S-1): 11 (2011) - [j12]Holger Gohlke, Alexander Metz, Christopher Pfleger, Dennis M. Krüger, Sina Kazemi
:
Towards targeting protein-protein interfaces with small molecules. J. Cheminformatics 3(S-1): 21 (2011) - [j11]Dennis M. Krüger, José Ignacio Garzón, P. C. Montes, Holger Gohlke:
Predicting protein-protein interactions with DrugScorePPI: fully-flexible docking, scoring, and in silico alanine-scanning. J. Cheminformatics 3(S-1): 36 (2011) - [j10]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): 1604-1622 (2011) - [j9]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): 2666-2679 (2011) - 2010
- [j8]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): 20 (2010) - [j7]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): 1489-1501 (2010) - [j6]Dennis M. Krüger, Holger Gohlke:
DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. Nucleic Acids Res. 38(Web-Server-Issue): 480-486 (2010)
2000 – 2009
- 2009
- [j5]Domingo González-Ruiz, Holger Gohlke:
Steering Protein-Ligand Docking with Quantitative NMR Chemical Shift Perturbations. J. Chem. Inf. Model. 49(10): 2260-2271 (2009) - 2007
- [j4]Patrick Pfeffer, Holger Gohlke:
DrugScoreRNAKnowledge-Based Scoring Function To Predict RNA-Ligand Interactions. J. Chem. Inf. Model. 47(5): 1868-1876 (2007) - [j3]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): 2383-2400 (2007) - 2005
- [j2]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): 1668-1688 (2005) - 2004
- [j1]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): 238-250 (2004)
Coauthor Index
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