Holger Gohlke
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Computer Science
Holger Gohlke's Degrees
- PhD Computer Science University of Potsdam
- Masters Computer Science University of Potsdam
- Bachelors Computer Science University of Potsdam
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(Suggest an Edit or Addition)Holger Gohlke's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- The Amber biomolecular simulation programs (2005) (7188)
- MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. (2012) (2274)
- Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. (2003) (964)
- Knowledge-based scoring function to predict protein-ligand interactions. (2000) (904)
- Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf (2004) (725)
- Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method (2012) (708)
- Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. (2002) (554)
- Assessing scoring functions for protein-ligand interactions. (2004) (429)
- A toolkit and benchmark study for FRET-restrained high-precision structural modeling (2012) (377)
- DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. (2005) (316)
- Target flexibility: an emerging consideration in drug discovery and design. (2008) (232)
- Statistical potentials and scoring functions applied to protein-ligand binding. (2001) (169)
- Targeting protein-protein interactions with small molecules: challenges and perspectives for computational binding epitope detection and ligand finding. (2006) (154)
- A natural coarse graining for simulating large biomolecular motion. (2006) (141)
- DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions (2010) (141)
- Histone deacetylase (HDAC) inhibitors with a novel connecting unit linker region reveal a selectivity profile for HDAC4 and HDAC5 with improved activity against chemoresistant cancer cells. (2013) (139)
- Protein rigidity and thermophilic adaptation (2011) (134)
- Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. (2016) (123)
- Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context. (2014) (121)
- DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. (2002) (113)
- Change in protein flexibility upon complex formation: Analysis of Ras‐Raf using molecular dynamics and a molecular framework approach (2004) (112)
- Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein-Protein Interface (2012) (112)
- Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors (2002) (112)
- Structure-based computational analysis of protein binding sites for function and druggability prediction. (2012) (104)
- Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials. (2003) (100)
- DrugScoreRNAKnowledge-Based Scoring Function To Predict RNA-Ligand Interactions (2007) (95)
- Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory (2006) (90)
- Sequencing of FIC1, BSEP and MDR3 in a large cohort of patients with cholestasis revealed a high number of different genetic variants. (2017) (89)
- Molecular recognition of RNA: challenges for modelling interactions and plasticity (2009) (88)
- A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas aestusnigri – Structural and Functional Insights (2020) (84)
- Docking into knowledge-based potential fields: a comparative evaluation of DrugScore. (2002) (83)
- Predicting binding modes, binding affinities and ‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function (2000) (80)
- FEW: A workflow tool for free energy calculations of ligand binding (2013) (80)
- CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function (2013) (77)
- Platelets contribute to amyloid-β aggregation in cerebral vessels through integrin αIIbβ3–induced outside-in signaling and clusterin release (2016) (76)
- NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins (2012) (74)
- Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function (2013) (73)
- Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding. (2009) (73)
- On the Effects of Reactive Oxygen Species and Nitric Oxide on Red Blood Cell Deformability (2018) (73)
- α5β1‐integrins are sensors for tauroursodeoxycholic acid in hepatocytes (2013) (71)
- PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building (2019) (63)
- A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins (2011) (61)
- Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis (2015) (56)
- Modulating protein-protein interactions: from structural determinants of binding to druggability prediction to application. (2012) (54)
- Structure of Aquifex aeolicus Argonaute Highlights Conformational Flexibility of the PAZ Domain as a Potential Regulator of RNA-induced Silencing Complex Function* (2007) (54)
- Resolving dynamics and function of transient states in single enzyme molecules (2018) (51)
- Trading off stability against activity in extremophilic aldolases (2016) (50)
- Effects of novel HDAC inhibitors on urothelial carcinoma cells (2018) (49)
- Synthesis and nicotinic binding studies on enantiopure diazine analogues of the novel (2-chloro-5-pyridyl)-9-azabicyclo[4.2.1]non-2-ene UB-165. (2002) (49)
- Targeting HSP90 dimerization via the C terminus is effective in imatinib-resistant CML and lacks the heat shock response. (2018) (47)
- Analyzing the flexibility of RNA structures by constraint counting. (2008) (46)
- Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins (2011) (46)
- Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio. (2012) (44)
- Global and local indices for characterizing biomolecular flexibility and rigidity (2013) (44)
- Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis (2016) (43)
- Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2 (2013) (42)
- Molecular dynamics simulations and structure-guided mutagenesis provide insight into the architecture of the catalytic core of the ectoine hydroxylase. (2014) (42)
- Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity. (2010) (42)
- Structural basis of lantibiotic recognition by the nisin resistance protein from Streptococcus agalactiae (2016) (41)
- Large‐scale comparison of protein essential dynamics from molecular dynamics simulations and coarse‐grained normal mode analyses (2010) (40)
- Systematic analysis of ATG13 domain requirements for autophagy induction (2018) (37)
- Amber 2015, University of California, San Francisco (2015) (36)
- Alkoxyurea-Based Histone Deacetylase Inhibitors Increase Cisplatin Potency in Chemoresistant Cancer Cell Lines. (2017) (36)
- 3D QSAR Analyses-Guided Rational Design of Novel Ligands for the (α4)2(β2)3 Nicotinic Acetylcholine Receptor (2003) (36)
- Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations (2017) (35)
- Converging a Knowledge-Based Scoring Function: DrugScore2018 (2018) (33)
- MMPBSA . py : An E ffi cient Program for End-State Free Energy Calculations (2012) (33)
- Elastic Potential Grids: Accurate and Efficient Representation of Intermolecular Interactions for Fully Flexible Docking (2009) (33)
- Rational design and diversity-oriented synthesis of peptoid-based selective HDAC6 inhibitors. (2016) (32)
- Steering Protein-Ligand Docking with Quantitative NMR Chemical Shift Perturbations (2009) (32)
- Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs (2010) (32)
- C-terminal modulators of heat shock protein of 90 kDa (HSP90): State of development and modes of action. (2019) (31)
- Automated and optimally FRET-assisted structural modeling (2019) (31)
- Biallelic mutation of human SLC6A6 encoding the taurine transporter TAUT is linked to early retinal degeneration (2019) (31)
- How Good Are State-of-the-Art Docking Tools in Predicting Ligand Binding Modes in Protein-Protein Interfaces? (2012) (31)
- Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality. (2008) (31)
- Structure and efflux mechanism of the yeast pleiotropic drug resistance transporter Pdr5 (2021) (30)
- Co-culture of the fungus Fusarium tricinctum with Streptomyces lividans induces production of cryptic naphthoquinone dimers (2019) (30)
- Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies (2016) (30)
- Rigidity theory for biomolecules: concepts, software, and applications (2017) (29)
- Arg149 is involved in switching the low affinity, open state of the binding protein AfProX into its high affinity, closed state. (2011) (29)
- Determinants of the Unexpected Stability of RNA Fluorobenzene Self Pairs (2008) (29)
- Constraint counting on RNA structures: linking flexibility and function. (2009) (29)
- Partially inserted nascent chain unzips the lateral gate of the Sec translocon (2019) (28)
- HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations (2010) (27)
- Resolving Hot Spots in the C-Terminal Dimerization Domain that Determine the Stability of the Molecular Chaperone Hsp90 (2014) (27)
- Synthesis, Biological Evaluation and Molecular Modeling of Substituted Indeno[1,2-b]indoles as Inhibitors of Human Protein Kinase CK2 (2015) (26)
- Protein Flexibility and Mobility in Structure-Based Drug Design (2007) (26)
- Binding Region of Alanopine Dehydrogenase Predicted by Unbiased Molecular Dynamics Simulations of Ligand Diffusion (2013) (26)
- Design, Multicomponent Synthesis, and Anticancer Activity of a Focused Histone Deacetylase (HDAC) Inhibitor Library with Peptoid-Based Cap Groups. (2017) (25)
- Interaction of Ochratoxin A and Its Thermal Degradation Product 2′R-Ochratoxin A with Human Serum Albumin (2018) (25)
- Mutational mapping of the transmembrane binding site of the G-protein coupled receptor TGR5 and binding mode prediction of TGR5 agonists. (2015) (25)
- TopModel: Template-based protein structure prediction at low sequence identity using top-down consensus and deep neural networks. (2020) (25)
- Interdependence of a mechanosensitive anion channel and glutamate receptors in distal wound signaling (2021) (24)
- TopScore: Using Deep Neural Networks and Large Diverse Data Sets for Accurate Protein Model Quality Assessment. (2018) (24)
- Improving binding mode predictions by docking into protein-specifically adapted potential fields. (2005) (23)
- Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations (2016) (23)
- The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae. (2012) (23)
- Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM (2016) (22)
- Target Flexibility in RNA-Ligand Docking Modeled by Elastic Potential Grids. (2011) (22)
- Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1 (2018) (22)
- Structural assemblies of the di- and oligomeric G-protein coupled receptor TGR5 in live cells: an MFIS-FRET and integrative modelling study (2016) (22)
- Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins (2020) (21)
- Ensemble- and Rigidity Theory-Based Perturbation Approach To Analyze Dynamic Allostery. (2017) (21)
- From Determinants of RUNX1/ETO Tetramerization to Small-Molecule Protein-Protein Interaction Inhibitors Targeting Acute Myeloid Leukemia (2013) (21)
- Determinants of FIV and HIV Vif sensitivity of feline APOBEC3 restriction factors (2016) (21)
- Efficient and robust analysis of biomacromolecular flexibility using ensembles of network topologies based on fuzzy noncovalent constraints. (2013) (19)
- A Membrane-proximal, C-terminal α-Helix Is Required for Plasma Membrane Localization and Function of the G Protein-coupled Receptor (GPCR) TGR5* (2013) (19)
- Cosolvent-Enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-Based Drug Design. (2019) (19)
- Calcium-Promoted Interaction between the C2-Domain Protein EHB1 and Metal Transporter IRT1 Inhibits Arabidopsis Iron Acquisition. (2019) (19)
- Understanding the Inhibitory Effect of Highly Potent and Selective Archazolides Binding to the Vacuolar ATPase (2012) (19)
- DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking (2014) (19)
- Time-resolved structural analysis of an RNA-cleaving DNA catalyst (2021) (18)
- Activation of Integrins by Urea in Perfused Rat Liver* (2010) (18)
- Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain (2019) (18)
- Extension of the free energy workflow FEW towards implicit solvent/implicit membrane MM-PBSA calculations. (2015) (18)
- Design and synthesis of novel Y-shaped barbituric acid derivatives as PPARγ activators. (2016) (17)
- EDTA aggregates induce SYPRO orange-based fluorescence in thermal shift assay (2017) (17)
- Synthesis of peptoid-based class I selective histone deacetylase inhibitors with chemosensitizing properties. (2019) (17)
- Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance‐dependent dielectric model (2012) (17)
- Chlorflavonin Targets Acetohydroxyacid Synthase Catalytic Subunit IlvB1 for Synergistic Killing of Mycobacterium tuberculosis. (2017) (16)
- Contribution of single amino acid and codon substitutions to the production and secretion of a lipase by Bacillus subtilis (2017) (16)
- Rigidity Theory-Based Approximation of Vibrational Entropy Changes upon Binding to Biomolecules. (2017) (16)
- Determinants of the species selectivity of oxazolidinone antibiotics targeting the large ribosomal subunit (2013) (15)
- Design and biological testing of peptidic dimerization inhibitors of human Hsp90 that target the C-terminal domain. (2016) (15)
- On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation (2018) (15)
- Relevance of N-terminal residues for amyloid-β binding to platelet integrin αIIbβ3, integrin outside-in signaling and amyloid-β fibril formation. (2018) (15)
- FK506 Resistance of Saccharomyces cerevisiae Pdr5 and Candida albicans Cdr1 Involves Mutations in the Transmembrane Domains and Extracellular Loops (2018) (15)
- Nutrient exchange in arbuscular mycorrhizal symbiosis from a thermodynamic point of view (2019) (15)
- Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase (2017) (15)
- Novel 3,4-Dihydroisocoumarins Inhibit Human P-gp and BCRP in Multidrug Resistant Tumors and Demonstrate Substrate Inhibition of Yeast Pdr5 (2019) (15)
- Quality Matters: Extension of Clusters of Residues with Good Hydrophobic Contacts Stabilize (Hyper)Thermophilic Proteins (2014) (14)
- Binding modes of thioflavin T and Congo red to the fibril structure of amyloid-β(1-42). (2020) (14)
- Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions (2007) (14)
- Resolving the Negative Potential Side (n-side) Water-accessible Proton Pathway of F-type ATP Synthase by Molecular Dynamics Simulations* (2012) (14)
- Structure of the Response Regulator NsrR from Streptococcus agalactiae, Which Is Involved in Lantibiotic Resistance (2016) (13)
- DrugScore PPI webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions (2010) (13)
- Chalcone-based Selective Inhibitors of a C4 Plant Key Enzyme as Novel Potential Herbicides (2016) (13)
- Discovery of new acetylcholinesterase inhibitors for Alzheimer’s disease: virtual screening and in vitro characterisation (2021) (13)
- Transport of Peptidomimetic Thrombin Inhibitors with a 3-Amidino-Phenylalanine Structure: Permeability and Efflux Mechanism in Monolayers of a Human Intestinal Cell Line (Caco-2) (2001) (13)
- TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction (2021) (12)
- Suppression of RUNX1/ETO oncogenic activity by a small molecule inhibitor of tetramerization (2017) (12)
- Modular Solid-Phase Synthesis of Teroxazoles as a Class of α-Helix Mimetics (2012) (12)
- VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability (2015) (12)
- Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ(2) Values. (2016) (12)
- α-Aminoxy Oligopeptides: Synthesis, Secondary Structure, and Cytotoxicity of a New Class of Anticancer Foldamers. (2016) (11)
- Structural and dynamic insights revealing how lipase binding domain MD1 of Pseudomonas aeruginosa foldase affects lipase activation (2020) (11)
- Fluorescent analogs of peptoid-based HDAC inhibitors: Synthesis, biological activity and cellular uptake kinetics. (2019) (11)
- Calcium-Promoted Interaction between the C2-Domain Protein EHB1 and Metal Transporter IRT1 Inhibits Arabidopsis Iron Acquisition1 (2019) (11)
- Exploiting the Link between Protein Rigidity and Thermostability for Data‐Driven Protein Engineering (2008) (11)
- In vitro and mouse in vivo characterization of the potent free fatty acid 1 receptor agonist TUG-469 (2013) (11)
- Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A (2020) (11)
- Protein-Ligand Interactions: GOHLKE:PROTEIN-LIGAND INT O-BK (2012) (11)
- Design, Synthesis, and Biological Evaluation of Simplified Side Chain Hybrids of the Potent Actin Binding Polyketides Rhizopodin and Bistramide (2015) (10)
- Glutamine synthetase as a central element in hepatic glutamine and ammonia metabolism: novel aspects (2021) (10)
- Posttranslational Modification of the NADP-Malic Enzyme Involved in C4 Photosynthesis Modulates the Enzymatic Activity during the Day (2019) (10)
- Isoform-specific Inhibition of N-methyl-D-aspartate Receptors by Bile Salts (2019) (10)
- Surprising Non-Additivity of Methyl-Groups in Drug-Kinase Interaction. (2019) (10)
- AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools. (2020) (10)
- Semisynthetic Analogs of the Antibiotic Fidaxomicin—Design, Synthesis, and Biological Evaluation (2020) (10)
- Understanding Receptor‐Ligand Interactions as a Prerequisite for—Virtual Screening (2000) (9)
- The tetrahydroxanthone-dimer phomoxanthone A is a strong inducer of apoptosis in cisplatin-resistant solid cancer cells. (2019) (9)
- Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization (2019) (9)
- 40 Years of Research on Polybrominated Diphenyl Ethers (PBDEs)—A Historical Overview and Newest Data of a Promising Anticancer Drug (2021) (9)
- Novel Fluorescent Cyclic Nucleotide Derivatives to Study CNG and HCN Channel Function. (2019) (9)
- The Membrane‐Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A (2019) (8)
- Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation (2018) (8)
- Identification of a conserved interface of HIV-1 and FIV Vifs with Cullin 5 (2017) (8)
- JAK2 p.G571S in B-cell precursor acute lymphoblastic leukemia: a synergizing germline susceptibility (2019) (8)
- On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase (2017) (8)
- Predicting transmembrane helix pair configurations with knowledge‐based distance‐dependent pair potentials (2008) (8)
- Aqueous ionic liquids redistribute local enzyme stability via long-range perturbation pathways (2021) (7)
- Basal Histamine H4 Receptor Activation: Agonist Mimicry by the Diphenylalanine Motif (2019) (7)
- Converging a knowledge-based scoring function: DrugScore (2018) (7)
- Reactive Metabolites from Thiazole-Containing Drugs: Quantum Chemical Insights into Biotransformation and Toxicity. (2021) (7)
- Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway (2021) (7)
- Human RAD52 – a novel player in DNA repair in cancer and immunodeficiency (2017) (7)
- Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch (2017) (7)
- Force field dependence of riboswitch dynamics. (2015) (7)
- Conformations and lipophilicity profiles of some cyclic β-(1→3)- and β-(1→6)-linked oligogalactofuranosides (1999) (7)
- Promiscuous esterases counterintuitively are less flexible than specific ones (2020) (7)
- Loop 1 of APOBEC3C regulates its antiviral activity against HIV-1. (2020) (7)
- Complex long-distance effects of mutations that confer linezolid resistance in the large ribosomal subunit (2015) (7)
- Characterization of the nucleotide-binding domain NsrF from the BceAB-type ABC-transporter NsrFP from the human pathogen Streptococcus agalactiae (2020) (6)
- The human platelet antigen-1b (Pro33) variant of αIIbβ3 allosterically shifts the dynamic conformational equilibrium of this integrin toward the active state (2018) (6)
- Evidence for a credit-card-swipe mechanism in the human PC floppase ABCB4. (2021) (6)
- Xanthone, benzophenone and bianthrone derivatives from the hypersaline lake-derived fungus Aspergillus wentii. (2019) (6)
- Critical assessment of structure-based approaches to improve protein resistance in aqueous ionic liquids by enzyme-wide saturation mutagenesis (2021) (6)
- Targeting spectrin redox switches to regulate the mechanoproperties of red blood cells (2020) (6)
- Redesigning Aldolase Stereoselectivity by Homologous Grafting (2016) (6)
- Substrate access mechanism in a novel membrane-bound phospholipase A of Pseudomonas aeruginosa concordant with specificity and regioselectivity (2021) (6)
- Phosphorylated tyrosine 93 of hepatitis C virus nonstructural protein 5A is essential for interaction with host c-Src and efficient viral replication (2019) (6)
- α-Aminoxy Peptoids: A Unique Peptoid Backbone with a Preference for cis-Amide Bonds. (2017) (6)
- DrugScorePPI for scoring protein-protein interactions: improving a knowledge-based scoring function by atomtype-based QSAR (2010) (5)
- Identification of a Conserved Interface of Human Immunodeficiency Virus Type 1 and Feline Immunodeficiency Virus Vifs with Cullin 5 (2017) (5)
- Mechanism of fully-reversible, pH-sensitive inhibition of human glutamine synthetase by tyrosine nitration. (2020) (5)
- Evidence for functional selectivity in TUDC- and norUDCA-induced signal transduction via α5β1 integrin towards choleresis (2020) (5)
- Can constraint network analysis guide the identification phase of KnowVolution? A case study on improved thermostability of an endo-β-glucanase (2020) (5)
- Design, synthesis and biological evaluation of β-peptoid-capped HDAC inhibitors with anti-neuroblastoma and anti-glioblastoma activity. (2019) (5)
- Dimerization energetics of the G‐protein coupled bile acid receptor TGR5 from all‐atom simulations (2019) (5)
- The Puzzle of Metabolite Exchange and Identification of Putative Octotrico Peptide Repeat Expression Regulators in the Nascent Photosynthetic Organelles of Paulinella chromatophora (2020) (5)
- Rational design and diversity-oriented synthesis of peptoid-based selective HDAC 6 inhibitors † (2016) (5)
- BILIARY DISEASE a 5 b 1-Integrins Are Sensors for Tauroursodeoxycholic Acid in Hepatocytes (2013) (5)
- A phospholipase B from Pseudomonas aeruginosa with activity towards endogenous phospholipids affects biofilm assembly. (2022) (5)
- Flexibility analysis of biomacromolecules with application to computer-aided drug design. (2012) (4)
- Posttranslational Modification of the NADP-Malic Enzyme Involved in C4 Photosynthesis Modulates the Enzymatic Activity during the Day. (2019) (4)
- Statics of Biomacromolecules (2011) (4)
- Multi-scale modelling of macromolecular conformational changes (2009) (4)
- The many facets of bile acids in the physiology and pathophysiology of the human liver (2021) (4)
- Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors (2012) (4)
- A promiscuous ancestral enzyme´s structure unveils protein variable regions of the highly diverse metallo-β-lactamase family (2021) (4)
- Small-molecule inhibitors of nisin resistance protein NSR from the human pathogen Streptococcus agalactiae. (2019) (4)
- Chapter 13:Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules (2012) (4)
- Thermodynamic profile of mutual subunit control in a heteromeric receptor (2021) (4)
- Design, synthesis, and conformational analysis of trispyrimidonamides as α-helix mimetics. (2014) (4)
- Towards Restoring Catalytic Activity of Glutamine Synthetase With a Clinically Relevant Mutation (2015) (4)
- TopProperty: Robust Metaprediction of Transmembrane and Globular Protein Features Using Deep Neural Networks. (2021) (3)
- Foamy Viruses, Bet, and APOBEC3 Restriction (2021) (3)
- Advances in molecular dynamics simulations and free-energy calculations relevant for drug design (2013) (3)
- Development of a Biosensor Platform for Phenolic Compounds Using a Transition Ligand Strategy. (2021) (3)
- 3D QSAR analyses-guided rational design of novel ligands for the (alpha4)2(beta2)3 nicotinic acetylcholine receptor. (2003) (3)
- Cell Type-Dependent Escape of Capsid Inhibitors by Simian Immunodeficiency Virus SIVcpz (2020) (3)
- Allosteric signaling in C-linker and cyclic nucleotide-binding domain of HCN2 channels. (2021) (3)
- Constraint Network Analysis : Exploiting the Link Between Protein Rigidity and Thermostability (2008) (3)
- Predicting protein-protein interactions with DrugScorePPI: fully-flexible docking, scoring, and in silico alanine-scanning (2011) (3)
- Structural, mechanistic, and physiological insights into phospholipase A-mediated membrane phospholipid degradation in Pseudomonas aeruginosa (2022) (3)
- TopDomain: Exhaustive Protein Domain Boundary Metaprediction Combining Multisource Information and Deep Learning. (2021) (3)
- Constraint counting on RNA and ribosomal structures: linking flexibility and function (2011) (3)
- Protein engineering for feedback resistance in 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (2022) (3)
- Novel intracellular phospholipase B from Pseudomonas aeruginosa with activity towards endogenous phospholipids affects biofilm assembly (2021) (3)
- Bile Acids and TGR5 (Gpbar1) Signaling (2020) (2)
- Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site. (2017) (2)
- Integrative dynamic structural biology unveils conformers essential for the oligomerization of a large GTPase (2020) (2)
- Development of a First-in-Class Small-Molecule Inhibitor of the C-Terminal Hsp90 Dimerization (2021) (2)
- Novel Recurrent Germline JAK2 G571S Variant in Childhood Acute B-Lymphoblastic Leukemia: A Double Hit One Pathway Scenario (2018) (2)
- Frontispiece: α‐Aminoxy Oligopeptides: Synthesis, Secondary Structure, and Cytotoxicity of a New Class of Anticancer Foldamers (2016) (2)
- Synthesis and Properties of Fluorinated Nucleobases in DNA and RNA (2013) (2)
- Loop 1 of APOBEC3C regulates its antiviral activity against HIV-1 (2020) (2)
- F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism (2021) (2)
- Posttranslational modification of the NADP-malic enzyme involved in C 4 photosynthesis 2 fine-tunes the enzymatic activity during the day 3 (2019) (2)
- Unsaturated fatty acids augment protein transport via the SecA:SecYEG translocon (2021) (2)
- Cumulative Submillisecond All-Atom Simulations of the Temperature-Induced Coil-to-Globule Transition of Poly(N-vinylcaprolactam) in Aqueous Solution (2020) (2)
- Glutamine synthetase mutations that cause glutamine deficiency: mechanistic insights from molecular dynamics simulations (2014) (2)
- MULTI-SCALE MODELING OF (2009) (2)
- Respiratory and C4-photosynthetic NAD-malic enzyme coexist in bundle sheath cells mitochondria and evolved via association of differentially adapted subunits (2021) (2)
- Evidence for a bacterial Lands cycle phospholipase A: Structural and mechanistic insights into membrane phospholipid remodeling (2021) (1)
- N6-modified cAMP derivatives that activate protein kinase A also act as full agonists of murine HCN2 channels (2019) (1)
- From Hansch‐Fujita Analysis to AFMoC: A Road to Structure‐Based QSAR (2012) (1)
- Abstract 9050: Drug-Drug Interactions Between Aspirin and NSAIDs are Predicted by Kinetics of Cyclooxygenase-1 Inhibition (2012) (1)
- D QSAR Analyses-Guided Rational Design of Novel Ligands for the ( r 4 ) 2 ( â 2 ) 3 Nicotinic Acetylcholine Receptor (1)
- Structural and Energetic Aspects of Protein-Ligand Binding in Drug Design (2000) (1)
- Pathways of inter- and intrasubunit allosteric signaling in the C-linker disk and cyclic nucleotide-binding domain of HCN2 channels (2020) (1)
- Mapping the helix arrangement of the reconstituted ETR1 ethylene receptor transmembrane domain by EPR spectroscopy (2022) (1)
- Analyzing Protein Rigidity for Understanding and Improving Thermal Adaptation (2011) (1)
- Towards targeting protein-protein interfaces with small molecules (2011) (1)
- Opposing Subunits Interact to Stabilize the Closed State in HCN2 Channels (2019) (1)
- Uncoupling the cAMP Binding Domain from the Channel Gate in HCN2 Channels (2019) (1)
- Structural features of FAP174, a MYCBP-1 orthologue from Chlamydomonas reinhardtii, revealed by computational and experimental analyses (2017) (1)
- High-precision FRET analysis of the G-protein coupled receptor TGR5 in live cells (2014) (1)
- 1 Automated and optimally FRET-assisted structural modeling (2019) (1)
- Recurrent Germline Variant in RAD21 Predisposes Children to Lymphoblastic Leukemia or Lymphoma (2022) (1)
- Molecular Geometries of Furanoid ß(1→3)- and ß(1→6)-Linked Cyclogalactins (1998) (1)
- High Precision FRET Analysis of the G-Protein Coupled Receptor TGR5 in Live Cells (2014) (1)
- Physiological, Biochemical, and Structural Bioinformatic Analysis of the Multiple Inositol Dehydrogenases from Corynebacterium glutamicum (2022) (1)
- Fluorophore‐Labeled Cyclic Nucleotides as Potent Agonists of Cyclic Nucleotide‐Regulated Ion Channels (2020) (1)
- Pyrazolidine‐3,5‐dione‐based inhibitors of phosphoenolpyruvate carboxylase as a new class of potential C4 plant herbicides (2017) (1)
- α5β1 integrins act as sensors for tauroursodeoxycholic acid in hepatocytes (2013) (1)
- Liver cell hydration and integrin signaling (2021) (1)
- Uncoupling of Voltage- and Ligand-Induced Activation in HCN2 Channels by Glycine Inserts (2022) (1)
- Molecular Modeling and Simulations of DNA and RNA: DNAzyme as a Model System. (2022) (1)
- Rational Design Yields Molecular Insights on Leaf-Binding of Anchor Peptides. (2022) (1)
- The first archaeal PET-degrading enzyme belongs to the feruloyl-esterase family (2022) (1)
- Protein–Ligand Interactions (2018) (1)
- TopEnzyme: a framework and database for structural coverage of the functional enzyme space (2022) (1)
- Influence of Sequence Variation on RNA 3WJ Helical Orientation Studied by High-Precision FRET (2020) (0)
- Enzymatic C3-Methylation of Indoles Using Methyltransferase PsmD─Crystal Structure, Catalytic Mechanism, and Preparative Applications (2022) (0)
- Book Review: Handbook of Chemoinformatics—From Data to Knowledge. Edited by Johann Gasteiger. (2004) (0)
- XXV International Bile Acid Meeting : Bile Acids in Health and Disease 2018 (2018) (0)
- 1093 ACTIVATION OF INTEGRINS BY UREA IN PERFUSED RAT LIVER (2011) (0)
- High-Precision FRET to Analyze the Architecture and Heterogeneity of RNA Junctions (2013) (0)
- Integrative Molecular Modelling of Biomolecules Guided by FRET Experiments (2018) (0)
- Spectroscopic and QM/MM studies of the Cu(I) binding site of the plant ethylene receptor ETR1 (2022) (0)
- Determining the molecular consequences of clinically relevant glutamine synthetase mutations (2015) (0)
- How Tertiary Interactions Between the L2 and L3 Loops Affect the Dynamics of the Distant Ligand Binding Site in the Guanine Sensing Riboswitch (2014) (0)
- Identification and Characterization of the Haloperoxidase VPO-RR from Rhodoplanes roseus by Genome Mining and Structure-Based Catalytic Site Mapping (2022) (0)
- Resolution of Maximum Entropy Method-Derived Posterior Conformational Ensembles of a Flexible System Probed by FRET and Molecular Dynamics Simulations. (2023) (0)
- Accurate Determination of the RNA Junctions via Single-Molecule High-Precision FRET Measurements (2016) (0)
- Solution structure of lipase binding domain LID1 of foldase from Pseudomonas aeruginosa (2018) (0)
- Running title : Force field dependence of riboswitch dynamics Force field dependence of riboswitch dynamics (2015) (0)
- On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation (2018) (0)
- Determinants of FIV and HIV Vif sensitivity of feline APOBEC3 restriction factors (2016) (0)
- Corrigendum: Trading off stability against activity in extremophilic aldolases (2016) (0)
- On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase (2017) (0)
- Mutasynthesis of new Cannabinoid-Derivatives as Potential Drug Candidates (2019) (0)
- The architecture of the 10‐23 DNAzyme and its implications for DNA‐mediated catalysis (2022) (0)
- Accurate Distance and Structure Determination of Three Different RNA Three-Way Junctions via High Precision FRET (2013) (0)
- Experimental validation of the predicted TGR5 binding mode model (2015) (0)
- TGR5 (GPBAR1) in the Liver (2020) (0)
- A novel binding site in the nicotinic acetylcholine receptor for MB327 can explain its allosteric modulation relevant for organophosphorus-poisoning treatment. (2023) (0)
- Functional and structural characterization of interactions between opposite subunits in HCN pacemaker channels (2020) (0)
- Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation (2018) (0)
- LISTER: Semi-automatic metadata extraction from annotated experiment documentation in eLabFTW (2023) (0)
- Single MHC‐I Expression Promotes Virus‐Induced Liver Immunopathology (2022) (0)
- Simulating Thioflavin T and Congo Red Binding to the Fibril Structure of Amyloid- β (1-42) (2019) (0)
- Corrigendum to: Posttranslational Modification of the NADP-Malic Enzyme Involved in C4 Photosynthesis Modulates the Enzymatic Activity during the Day. (2021) (0)
- Supplementary Information (2021) (0)
- Visualizing Structures, Dynamics and Function of Enzymes (2014) (0)
- Conformational Fluctuations as an Intrinsic Mechanism of Action of Lipase Foldase Studied by the High-Precision FRET Toolkit and MD Simulations (2015) (0)
- Mapping Motions and Structure to a State Necessary for Oligomerization of a Large GTPase: A Joint SAXS, NSE, EPR and FRET Study (2016) (0)
- Conformational Entropy of the RNA Phosphate-Sugar Backbone (2014) (0)
- α5β1 integrins in hepatocytes act as receptors for bile acids with a (nor)ursodeoxycholane scaffold (2014) (0)
- Respiratory and C4-photosynthetic NAD-malic enzyme coexist in bundle sheath cell mitochondria and evolved via association of differentially adapted subunits. (2021) (0)
- High-Precision FRET Reveals Sequence Dependent Structures of RNA Three-Way Junctions (2019) (0)
- Erratum: "AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools" [J. Chem. Phys. 152, 221103 (2020)]. (2021) (0)
- Loading and Co-Solvent-Triggered Release of Okanin, a C4 Plant Key Enzyme Inhibitor, into/from Functional Microgels (2023) (0)
- Structure and Function of Redox-Sensitive Superfolder Green Fluorescent Protein Variant (2022) (0)
- Vasor: Accurate prediction of variant effects for amino acid substitutions in MDR3 (2022) (0)
- The secondary structure of the TGR5 membrane-proximal C-terminus determines plasma membrane localization and responsiveness towards extracellular ligands (2014) (0)
- Tailoring Acetaldehyde Dependent Aldolases for Organic Synthesis (2013) (0)
- Transient Pocket Identification and Evaluation of their Role for Allostery (2018) (0)
- Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins (2020) (0)
- A promiscuous ancestral enzyme´s structure unveils protein variable regions of the highly diverse metallo-β-lactamase family (2021) (0)
- Vasor: Accurate prediction of variant effects for amino acid substitutions in multidrug resistance protein 3 (2022) (0)
- In vitro and in silico characterization of a novel NR1H4/FXR mutation causing Progressive Familial Intrahepatic Cholestasis Type 5 (2022) (0)
- Protein Structure Determination by High-Precision FRET and Molecular Modeling (2017) (0)
- FRET, SAXS and Molecular Simulations Resolve the Solution Structures of Three Coexisting Conformers of Flexible RNA Four-Way Junction (2017) (0)
- P1266 A MEMBRANE-PROXIMAL C-TERMINAL a-HELIX IS REQUIRED FOR GPCR TRAFFICKING TO THE CELL SURFACE (2014) (0)
- Biophysical and pharmacokinetic characterization of a small-molecule inhibitor of RUNX1/ETO tetramerization with anti-leukemic effects (2021) (0)
- Structure of Aquifex aeolicus Argonuate (2007) (0)
- Diagnostic workup of suspected hereditary cholestasis in adults: a case report (2023) (0)
- Foreword. (2020) (0)
- The human platelet antigen-1 b ( Pro 33 ) variant of IIb 3 allosterically shifts the dynamic conformational (2018) (0)
- Resolving dynamics and function of transient states in single enzyme molecules (2020) (0)
- Total Synthesis of the Antimycobacterial Natural Product Chlorflavonin and Analogs via a Late-Stage Ruthenium(II)-Catalyzed ortho-C(sp2)-H-Hydroxylation (2022) (0)
- Binding Free Energy Calculations and Molecular Dynamics Studies on Complexes of Viral Proteases with their Ligands Inaugural (2013) (0)
- Protein Flexibility in In Silico Screening (2010) (0)
- Atomic Resolution Insights into pH Shift Induced Deprotonation Events in LS-Shaped Aβ(1–42) Amyloid Fibrils (2023) (0)
- Design and synthesis of novel Y-shaped barbituric acid derivatives as PPAR g activators (2015) (0)
- Effect of AU Substitutions at the Stem on the Stability of Kissing Loop Complexes (2013) (0)
- Effects of novel HDAC inhibitors on urothelial carcinoma cells (2018) (0)
- Molecular Mechanisms Underlying Medium-Chain Length Free Fatty Acid-regulated Activity of the Phospholipase PlaF from P. aeruginosa (2023) (0)
- Predicting Protein-protein Interactions with DrugScorePPI : Docking , Scoring , and in silico Alanine-scanning (2011) (0)
- Supporting a novel plant protection technology by molecular dynamics simulations (2020) (0)
- α5β1 Integrins are Receptors for Bile Acids with a (Nor-)Ursodeoxycholane Scaffold (2015) (0)
- Structure and properties of the selectivity filter of homo- and hetero- tetrameres of plant ionotropic glutamate receptors: a modelling approach (2022) (0)
- The Role of Cytoskeletal S-Nitrosation in Red Blood Cell Deformability (2016) (0)
- Therapeutic Targeting of HSP90 in AML and ALL (2018) (0)
- Structure and dynamics of lipase specific foldase from Pseudomonas aeruginosa (2015) (0)
- Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions (2022) (0)
- Met/Val129 polymorphism of the full-length human prion protein dictates distinct pathways of amyloid formation (2022) (0)
- Isoform-specific Inhibition of N-methyl-D-aspartate Receptors by Bile Salts (2019) (0)
- Polaro-graphic and photometric estimation of tocopherono-lactone in aqueous solution using thin-layer chromato-graphy. (1965) (0)
- Novel binding pocket descriptors based on DrugScore potential fields encoded by 3D Zernike descriptors (2012) (0)
- Unravelling the Di- and Oligomerisation Interfaces of the G-Protein Coupled Bile Acid Receptor TGR5 via Integrative Modelling (2018) (0)
- Toolkit for Multi-Conformation Biomolecular Structure Determination by High-Precision FRET and Molecular Simulations (2015) (0)
- Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1 (2018) (0)
- Determining RNA Flexibility by Graph Theory : Ribosomal Exit Tunnel as a Case Study (2008) (0)
- Integrative Dynamic Structural Biology with Fluorescence Spectroscopy (2019) (0)
- RNA Junctions Structure and Distance Determination via Accurate Single-Molecule High-Precision FRET Measurements (2015) (0)
- Binding Mode Prediction and Validation of Bile Acid and Neurosteroid Agonists of TGR5 (2015) (0)
- [Polarographic and photometric determination of tocopheronolactone in aqueous solution following the use of thin-layer chromatography]. (1965) (0)
- Time-resolved structural analysis of an RNA-cleaving DNA catalyst (2021) (0)
- Rational design yields molecular insights on leaf binding of the anchor peptide Macaque Histatin (2022) (0)
- A proximal α-helix of the TGR5 C-Terminus is essential for receptor plasma membrane localization (2014) (0)
- Topology of Large RNA Junctions Explored by High-Precision FRET (2014) (0)
- Molecular modeling of saccharides, 22. Conformations and lipophilicity profiles of some cyclic ß-(1->6)-linked oligogalactofuranosides (1999) (0)
- FRET-Assisted Protein Structure Postdiction of CASP13 Targets (2020) (0)
- Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes (2023) (0)
- A MademoiseLLE domain binding platform links the key RNA transporter to endosomes (2021) (0)
- Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain (2019) (0)
- Conformational Fluctuations as an Intrinsic Mechanism of Action: The Lipase-Specific Foldase of Pseudomonas Aeruginosa Studied by Hybrid Fluorescence Spectroscopy and MD Simulations (2017) (0)
- FAP 174 , a MYCBP-1 orthologue from Chlamydomonas reinhardtii , revealed by computational and experimental analyses † (2017) (0)
- Quantitative Characterization of the Conformational Dynamics of the Unbound Lipase-specific Foldase Lif by MD Simulations and Fluorescence Spectroscopy (2018) (0)
- Fatty acids and phospholipids as Regulators of Pseudomonas aeruginosa phospholipase PlaF function (2018) (0)
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