We propose a simple model for the calculation of pK(a) values of ionizable residues in proteins. It is based on the premise that the pK(a) shift of ionizable residues is linearly correlated to the interaction between a particular residue and the local environment created by the surrounding residues. Despite its simplicity, the model displays good prediction performance. Under the sixfold cross ...

A protocol for the ab initio crystal structure determination of powdered solids at natural isotopic abundance by combining solid-state NMR spectroscopy, crystal structure prediction, and DFT chemical shift calculations was evaluated to determine the crystal structures of four small drug molecules: cocaine, flutamide, flufenamic acid, and theophylline. For cocaine, flutamide and flufenamic acid,...

Searching for well-fitting 3D oligopeptide fragments within a large collection of protein structures is an important task central to many analyses involving protein structures. This article reports a new web server, Super, dedicated to the task of rapidly screening the protein data bank (PDB) to identify all fragments that superpose with a query under a prespecified threshold of root-mean-squar...

Computational docking of small-molecule ligands into protein receptors is an important tool for modern drug discovery. Although conformational adjustments are frequently observed between the free and ligand-bound states, the conformational flexibility of the protein is typically ignored in protein-small molecule docking programs. We previously described the program RosettaLigand, which leverage...

In order to characterize molecular structures we introduce configurational fingerprint vectors which are counterparts of quantities used experimentally to identify structures. The Euclidean distance between the configurational fingerprint vectors satisfies the properties of a metric and can therefore safely be used to measure dissimilarities between configurations in the high dimensional config...

In this work we have implemented and analyzed the performance of a new real coded steady-state genetic algorithm (SSGA) for the flexible ligand-receptor docking problem. The algorithm employs a grid-based methodology, considering the receptor rigid, and the GROMOS classical molecular force field to evaluate the energy function. In the implementation we used the restricted tournament selection (...

A new approach in determining local residue flexibility from base-amino acid contact frequencies is applied to the twelve million lattice chains modeling BIV Tat peptide binding to TAR RNA fragment. Many of the resulting key features in flexibility correspond to RMSD calculations derived from a set of five NMR derived structures (X. Ye, R. A. Kumar, and D. J. Patel, Protein Data Bank: Database ...

Precipitation is an essential climate and forcing variable for modeling the global water cycle. Particularly, recent Integrated Multi-satellite Retrievals GPM (IMERG) product retrospectively provides unprecedented two decades of high-resolution satellite precipitation estimates. The primary goal this study to examine similarities differences between latest also arguably most popular, IMERG Earl...