| Mechanisms of antibiotic resistance: QM/MM modeling of the acylation reaction of a class A β-lactamase with benzylpenicillin JC Hermann, C Hensen, L Ridder, AJ Mulholland, HD Höltje Journal of the American Chemical Society 127 (12), 4454-4465, 2005 | 177 | 2005 |
| Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships F Huber, L Ridder, S Verhoeven, JH Spaaks, F Diblen, S Rogers, ... PLoS computational biology 17 (2), e1008724, 2021 | 175 | 2021 |
| Aromatic hydroxylation by cytochrome P450: model calculations of mechanism and substituent effects CM Bathelt, L Ridder, AJ Mulholland, JN Harvey Journal of the American Chemical Society 125 (49), 15004-15005, 2003 | 160 | 2003 |
| Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake JJJ van der Hooft, RCH de Vos, V Mihaleva, RJ Bino, L Ridder, N de Roo, ... Analytical Chemistry 84 (16), 7263-7271, 2012 | 157 | 2012 |
| SyGMa: combining expert knowledge and empirical scoring in the prediction of metabolites L Ridder, M Wagener ChemMedChem: Chemistry Enabling Drug Discovery 3 (5), 821-832, 2008 | 154 | 2008 |
| Substructure‐based annotation of high‐resolution multistage MSn spectral trees L Ridder, JJJ van der Hooft, S Verhoeven, RCH de Vos, R van Schaik, ... Rapid Communications in Mass Spectrometry 26 (20), 2461-2471, 2012 | 153 | 2012 |
| Mechanism and structure–reactivity relationships for aromatic hydroxylation by cytochrome P450 CM Bathelt, L Ridder, AJ Mulholland, JN Harvey Organic & Biomolecular Chemistry 2 (20), 2998-3005, 2004 | 145 | 2004 |
| Automatic Chemical Structure Annotation of an LC–MSn Based Metabolic Profile from Green Tea L Ridder, JJJ van der Hooft, S Verhoeven, RCH de Vos, RJ Bino, ... Analytical Chemistry 85 (12), 6033-6040, 2013 | 130 | 2013 |
| Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction KE Ranaghan, L Ridder, B Szefczyk, WA Sokalski, JC Hermann, ... Organic & biomolecular chemistry 2 (7), 968-980, 2004 | 126 | 2004 |
| A community resource for paired genomic and metabolomic data mining MA Schorn, S Verhoeven, L Ridder, F Huber, DD Acharya, AA Aksenov, ... Nature Chemical Biology 17 (4), 363-368, 2021 | 121 | 2021 |
| A quantum mechanical/molecular mechanical study of the hydroxylation of phenol and halogenated derivatives by phenol hydroxylase L Ridder, AJ Mulholland, IMCM Rietjens, J Vervoort Journal of the American Chemical Society 122 (36), 8728-8738, 2000 | 109 | 2000 |
| MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra F Huber, S van der Burg, JJJ van der Hooft, L Ridder Journal of cheminformatics 13 (1), 84, 2021 | 108 | 2021 |
| Sleep classification from wrist-worn accelerometer data using random forests K Sundararajan, S Georgievska, BHW Te Lindert, PR Gehrman, ... Scientific reports 11 (1), 24, 2021 | 107 | 2021 |
| Automatic compound annotation from mass spectrometry data using MAGMa L Ridder, JJJ van der Hooft, S Verhoeven Mass Spectrometry 3 (Special_Issue_2), S0033-S0033, 2014 | 96 | 2014 |
| Identification of Glu166 as the general base in the acylation reaction of class A β-lactamases through QM/MM modeling JC Hermann, L Ridder, AJ Mulholland, HD Höltje Journal of the American Chemical Society 125 (32), 9590-9591, 2003 | 95 | 2003 |
| Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9, 10-oxide L Ridder, IMCM Rietjens, J Vervoort, AJ Mulholland Journal of the American Chemical Society 124 (33), 9926-9936, 2002 | 94 | 2002 |
| DeepRank: a deep learning framework for data mining 3D protein-protein interfaces N Renaud, C Geng, S Georgievska, F Ambrosetti, L Ridder, DF Marzella, ... Nature communications 12 (1), 7068, 2021 | 90 | 2021 |
| Insights into enzyme catalysis from QM/MM modelling: transition state stabilization in chorismate mutase KE Ranaghan, L Ridder, B Szefczyk, WA Sokalski, JC Hermann, ... Molecular Physics 101 (17), 2695-2714, 2003 | 90 | 2003 |
| Molecular mechanisms of antibiotic resistance: QM/MM modelling of deacylation in a class A β-lactamase JC Hermann, L Ridder, HD Höltje, AJ Mulholland Organic & biomolecular chemistry 4 (2), 206-210, 2006 | 87 | 2006 |
| Ab initio QM/MM modeling of the hydroxylation step in p-hydroxybenzoate hydroxylase L Ridder, JN Harvey, IMCM Rietjens, J Vervoort, AJ Mulholland The Journal of Physical Chemistry B 107 (9), 2118-2126, 2003 | 84 | 2003 |
