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BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers, which supports a wide range of identifiers from the most used biological databases currently available. Expand
Benchmarking ortholog identification methods using functional genomics data
By combining the sensitivity and the selectivity into an overall score, it is shown that the InParanoid program is the best ortholog identification method in terms of identifying functionally equivalent proteins. Expand
Steroid and G protein binding characteristics of the seatrout and human progestin membrane receptor alpha subtypes and their evolutionary origins.
Phylogenetic analysis indicates the mPRs are members of a progesterone and adipoQ receptor (PAQR) subfamily that is only present in chordates, whereas other PAQRs also occur in invertebrates and plants. Expand
A flexible approach to induced fit docking.
- S. Nabuurs, M. Wagener, J. de Vlieg
- Chemistry, Medicine
- Journal of medicinal chemistry
- 22 November 2007
Fleksy produces a set of receptor-ligand complexes ranked using a consensus scoring function combining docking scores and force field energies, which compares favorably to the rigid receptor FlexX program, which on average reaches a success rate of 44% for these datasets. Expand
Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor
This study on prednisolone-induced effects in livers of WT and GRdim mice identified a number of interesting candidate genes and pathways regulated by GR dimers and sheds new light onto the complex transcriptional regulation of liver function by GCs. Expand
Dynamics of Fusarium solani cutinase investigated through structural comparison among different crystal forms of its variants
Because of the availability of a set of closely related proteins in different crystal environments, the intrinsic drawback of a crystallographic approach was bypassed and the dynamics of the protein could be monitored much more realistically than what can be achieved on the basis of static pictures alone. Expand
Data-driven medicinal chemistry in the era of big data.
- S. Lusher, R. McGuire, René C van Schaik, C. D. Nicholson, J. de Vlieg
- Computer Science, Medicine
- Drug discovery today
- 1 July 2014
Data-driven medicinal chemistry approaches have the potential to improve decision making in drug discovery projects, providing that all researchers embrace the role of 'data scientist' and uncover the meaningful relationships and patterns in available data. Expand
Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state.
It is suggested on the basis of a covalently bond inhibitor that the cutinase oxyanion hole may consist not only of two main chain amide groups but also of the Ser42 O gamma side chain, which is characterized by the triad Ser, His, and Asp (Glu) residues. Expand
Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations
- L. Creveld, A. Amadei, R. V. van Schaik, H. Pepermans, J. de Vlieg, H. Berendsen
- Chemistry, Medicine
- 1 November 1998
Computer simulations on cutinase and analysis procedures are presented to distinguish the movements related to its functional behavior from those related to the unfolding of the enzyme, suggesting that mutations in the regions involved might stabilize the enzyme without affecting its functionality. Expand
Structural Basis for Agonism and Antagonism for a Set of Chemically Related Progesterone Receptor Modulators
- S. Lusher, H. Raaijmakers, +9 authors J. de Vlieg
- Chemistry, Medicine
- The Journal of Biological Chemistry
- 17 August 2011
Two new progesterone receptor ligand binding domain x-ray structures bound to compounds from a structurally related but functionally divergent series, which show different binding modes corresponding to their agonistic or antagonistic nature. Expand