Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a n...

Quantitative estimation of the magnitude and variability of gross primary productivity (GPP) is required to study the carbon cycle of the terrestrial ecosystem. Using ecosystem models and remotely-sensed data is a practical method for accurately estimating GPP. This study presents a method for assimilating high-quality leaf area index (LAI) products retrieved from satellite data into a process-...

UNLABELLED Nitrogen is one of the major growth-limiting nutrients for plants: The main source of nitrogen in most of the higher plants is nitrate taken up through roots. Nitrate can be reduced both in the chloroplasts (photosynthetic tissues) and in proplastes (nonphotosynthetic tissues) such as roots. Ferredoxin-nitrite reductase (NiR) catalyses the reduction of nitrite to ammonium in the seco...

We have developed a new method for predicting helix positions in globular proteins that is intended primarily for comparative modeling and other applications where high precision is required. Unlike helix packing algorithms designed for ab initio folding, we assume that knowledge is available about the qualitative placement of all helices. However, even among homologous proteins, the correspond...

MOTIVATION Meaningful scores to assess protein structure similarity are essential to decipher protein structure and sequence evolution. The mining of the increasing number of protein structures requires fast and accurate similarity measures with statistical significance. Whereas numerous approaches have been proposed for protein domains as a whole, the focus is progressively moving to a more lo...

The predictive modeling and design of biologically active RNA molecules requires understanding the energetic balance among their basic components. Rapid developments in computer simulation promise increasingly accurate recovery of RNA's nearest-neighbor (NN) free-energy parameters, but these methods have not been tested in predictive trials or on nonstandard nucleotides. Here, we present, to ou...

Complete List of Authors: Bagaria, Anurag; Goethe-Universität Frankfurt am Main, Institut für Biophysikalische Chemie Jaravine, Victor; Goethe-Universität Frankfurt am Main, Institut für Biophysikalische Chemie Huang, Yuanpeng; Rutgers University, Department of Molecular Biology and Biochemistry Montelione, Gaetano; Rutgers University, Department of Molecular Biology and Biochemistry Güntert, P...

BACKGROUND Most of the objective and quantitative methods proposed for spasticity measurement are not suitable for clinical application, and methods for surface electromyography (sEMG) signal processing are mainly limited to the time-domain. This study aims to quantify muscle activity in the time-frequency domain, and develop a practical clinical method for the objective and reliable evaluation...

The TASSER structure prediction algorithm is employed to investigate whether NMR structures can be moved closer to their corresponding X-ray counterparts by automatic refinement procedures. The benchmark protein dataset includes 61 nonhomologous proteins whose structures have been determined by both NMR and X-ray experiments. Interestingly, by starting from NMR structures, the majority (79%) of...

We have developed a generic evolutionary method with an empirical scoring function for the protein-ligand docking, which is a problem of paramount importance in structure-based drug design. This approach, referred to as the GEMDOCK (Generic Evolutionary Method for molecular DOCKing), combines both continuous and discrete search mechanisms. We tested our approach on seven protein-ligand complexe...