Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers).

Effect of Wave Process of Plastic Deformation at Forging on the Fatigue Fracture Mechanism of Titanium Compressor Disks of Gas Turbine Engine.

The low-cycle fatigue behavior of the VT3-1 titanium alloy (Ti-6Al-3Mo-2Cr alloy) under loading with a triangular and trapezoidal shape of cycle waveform was studied on round specimens prepared from forged compressor disks of a gas turbine engine. The filament type structure after forging has alternating filaments with the ductile and quasi-brittle state of the metal as a result of the wave process of plastic deformation during the metal forging process. The crack propagation, regardless of the cyclic waveform shape, occurs by the crack meso-tunneling mechanism: initially, the cracks propagate along the filaments by a quasi-brittle mechanism with the formation of a facetted pattern relief on the fracture surface reflecting the two-phase structure of the titanium alloy, and then, the bridge between the meso-tunnels is fractured with the formation of fatigue striations.

Protein-Protein and Protein-Peptide Docking with ClusPro Server.

The process of creating a model of the structure formed by a pair of interacting molecules is commonly referred to as docking. Protein docking is one of the most studied topics in computational and structural biology with applications to drug design and beyond. In this chapter, we describe ClusPro, a web server for protein-protein and protein-peptide docking.

ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.

Targets in the protein docking experiment CAPRI (Critical Assessment of Predicted Interactions) generally present new challenges and contribute to new developments in methodology. In rounds 38 to 45 of CAPRI, most targets could be effectively predicted using template-based methods. However, the server ClusPro required structures rather than sequences as input, and hence we had to generate and dock homology models.

Dynamics of supernova bounce in laboratory.

We draw attention to recent high-explosive (HE) experiments which provide compression of macroscopic amount of matter to high, even record, values of pressure in comparison with other HE experiments. The observed bounce after the compression corresponds to processes in core-collapse supernova explosions after neutrino trapping. Conditions provided in the experiments resemble those in core-collapse supernovae, permitting their use for laboratory astrophysics.

Protein-ligand docking using FFT based sampling: D3R case study.

Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein-protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein-peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein-ligand interactions in application to the D3R PL-2016-1 challenge.

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds.

Energy evaluation using fast Fourier transforms (FFTs) enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods, efficient acceleration is achieved only in either the translational or the rotational subspace. Developing an efficient and accurate docking method that expands FFT-based sampling to five rotational coordinates is an extensively studied but still unsolved problem.

SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies.

Hydrodynamic interactions (HI) are incorporated into Langevin dynamics of the Cα -based protein model using the Truncated Expansion approximation (TEA) to the Rotne-Prager-Yamakawa diffusion tensor. Computational performance of the obtained GPU realization demonstrates the model's capability for describing protein systems of varying complexity (10(2) -10(5) residues), including biological particles (filaments, virus shells). Comparison of numerical accuracy of the TEA versus exact description of HI reveals similar results for the kinetics and thermodynamics of protein unfolding.

Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles.

The mechanical properties of virus capsids correlate with local conformational dynamics in the capsid structure. They also reflect the required stability needed to withstand high internal pressures generated upon genome loading and contribute to the success of important events in viral infectivity, such as capsid maturation, genome uncoating and receptor binding. The mechanical properties of biological nanoparticles are often determined from monitoring their dynamic deformations in Atomic Force Microscopy nanoindentation experiments; but a comprehensive theory describing the full range of observed deformation behaviors has not previously been described.

[Role of measurement of fractional flow reserve in coronary artery atherosclerosis].

The paper considers coronary flow in health and coronary flow autoregulation in health and disease. It gives basic methods used to estimate coronary flow reserve in patients with coronary atherosclerosis. The physiological bases for determining fractional flow reserve are presented.