The work reports validation of numerical weather forecasts (NWF), QuikSCAT-based wind speed and AMSR-E sea surface temperature (SST) for the surface atmospheric boundary layer in the Indian sector of the Southern Ocean under the International Polar Year. The database consists of wind speed, air temperature, relative humidity, sea level pressure collected along the ship route from Durban (32.4°S...

Exhaustive exploration of molecular interactions at the level of complete proteomes requires efficient and reliable computational approaches to protein function inference. Ligand docking and ranking techniques show considerable promise in their ability to quantify the interactions between proteins and small molecules. Despite the advances in the development of docking approaches and scoring fun...

To generate structures consistent with both the local and nonlocal interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons et al., J Mol Biol 1997; 268:209-225). The scoring function used in the simul...

Computational protein tertiary structure prediction has made significant progress over the past years. However, most of the existing structure prediction methods are not equipped with functionality to predict accuracy of constructed models. Knowing the accuracy of a structure model is crucial for its practical use since the accuracy determines potential applications of the model. Here we have d...

We describe the development of new force fields for protein side chain modeling called optimized side chain atomic energy (OSCAR). The distance-dependent energy functions (OSCAR-d) and side-chain dihedral angle potential energy functions were represented as power and Fourier series, respectively. The resulting 802 adjustable parameters were optimized by discriminating the native side chain conf...

Structure comparisons of all representative proteins have been done. Employing the relative root mean square deviation (RMSD) from native enables the assessment of the statistical significance of structure alignments of different lengths in terms of a Z-score. Two conclusions emerge: first, proteins with their native fold can be distinguished by their Z-score. Second and somewhat surprising, al...

Cold thermoregulatory models (CTM) have primarily been developed to predict core temperature (T(core)) responses during sedentary immersion. Few studies have examined their efficacy to predict T(core) during exercise cold exposure. The purpose of this study was to compare observed T(core) responses during exercise in cold water with the predicted T(core) from a three-cylinder (3-CTM) and a six-...

Published two-body bond-valence parameters for cation-oxygen bonds have been evaluated via the root mean-square deviation (RMSD) from the valence-sum rule for 128 cations, using 180,194 filtered bond lengths from 31,489 coordination polyhedra. Values of the RMSD range from 0.033-2.451 v.u. (1.1-40.9% per unit of charge) with a weighted mean of 0.174 v.u. (7.34% per unit of charge). The set of b...

A common strategy for virtual screening considers a systematic docking of a large library of organic compounds into the target sites in protein receptors with promising leads selected based on favorable intermolecular interactions. Despite a continuous progress in the modeling of protein-ligand interactions for pharmaceutical design, important challenges still remain, thus the development of no...