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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.
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.
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.
A flexible approach to induced fit docking.
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.
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.
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.
Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations
- L. Creveld, A. Amadei, R. van Schaik, H. Pepermans, J. de Vlieg, H. Berendsen
- 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.
Testing statistical significance scores of sequence comparison methods with structure similarity
- Tim Hulsen, J. de Vlieg, J. Leunissen, P. Groenen
- Computer Science, MedicineBMC Bioinformatics
- 12 October 2006
Two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith- waterman implementation with Z-score, and the compute intensive Z- score does not have a clear advantage over the e- value.
Data-driven medicinal chemistry in the era of big data.
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.