2020
Metadynamics as a Postprocessing Method for Virtual Screening with Application to the Pseudokinase Domain of JAK2
Cutrona KJ, Newton AS, Krimmer SG, Tirado-Rives J, Jorgensen WL. Metadynamics as a Postprocessing Method for Virtual Screening with Application to the Pseudokinase Domain of JAK2. Journal Of Chemical Information And Modeling 2020, 60: 4403-4415. PMID: 32383599, PMCID: PMC7927942, DOI: 10.1021/acs.jcim.0c00276.Peer-Reviewed Original ResearchSelective Janus Kinase 2 (JAK2) Pseudokinase Ligands with a Diaminotriazole Core
Liosi ME, Krimmer SG, Newton AS, Dawson T, Puleo DE, Cutrona KJ, Suzuki Y, Schlessinger J, Jorgensen WL. Selective Janus Kinase 2 (JAK2) Pseudokinase Ligands with a Diaminotriazole Core. Journal Of Medicinal Chemistry 2020, 63: 5324-5340. PMID: 32329617, PMCID: PMC7949251, DOI: 10.1021/acs.jmedchem.0c00192.Peer-Reviewed Original Research
2018
Bayesian analysis of isothermal titration calorimetry for binding thermodynamics
Nguyen T, Rustenburg A, Krimmer S, Zhang H, Clark J, Novick P, Branson K, Pande V, Chodera J, Minh D. Bayesian analysis of isothermal titration calorimetry for binding thermodynamics. PLOS ONE 2018, 13: e0203224. PMID: 30212471, PMCID: PMC6136728, DOI: 10.1371/journal.pone.0203224.Peer-Reviewed Original ResearchOptimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor
Trivedi‐Parmar V, Robertson MJ, Cisneros J, Krimmer SG, Jorgensen WL. Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor. ChemMedChem 2018, 13: 1092-1097. PMID: 29575754, PMCID: PMC5990473, DOI: 10.1002/cmdc.201800158.Peer-Reviewed Original Research
2016
Six Biophysical Screening Methods Miss a Large Proportion of Crystallographically Discovered Fragment Hits: A Case Study
Schiebel J, Radeva N, Krimmer S, Wang X, Stieler M, Ehrmann F, Fu K, Metz A, Huschmann F, Weiss M, Mueller U, Heine A, Klebe G. Six Biophysical Screening Methods Miss a Large Proportion of Crystallographically Discovered Fragment Hits: A Case Study. ACS Chemical Biology 2016, 11: 1693-1701. PMID: 27028906, DOI: 10.1021/acschembio.5b01034.Peer-Reviewed Original ResearchImpact of Surface Water Layers on Protein–Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case?
Betz M, Wulsdorf T, Krimmer S, Klebe G. Impact of Surface Water Layers on Protein–Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case? Journal Of Chemical Information And Modeling 2016, 56: 223-233. PMID: 26691064, DOI: 10.1021/acs.jcim.5b00621.Peer-Reviewed Original ResearchConceptsObserved structure-activity relationshipsLocal water structureProtein-ligand bindingMolecular dynamics simulationsStructure-activity relationshipsHigh-resolution crystal structuresSolvation sitesWater structureSurface water networkWater rearrangementCrystal structureDesolvation effectsDifference electronMolecular dynamicsDynamics simulationsLigand portionWater networkDrug bindingContribution of waterWater layerComplexesSurface water layerWaterPhosphonamidatesStructure
2015
Thermodynamics of protein–ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data
Krimmer S, Klebe G. Thermodynamics of protein–ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data. Journal Of Computer-Aided Molecular Design 2015, 29: 867-883. PMID: 26376645, DOI: 10.1007/s10822-015-9867-y.Peer-Reviewed Original Research