A fast algorithm for generating smooth molecular dot surface representations

An update on vascular calcification and potential therapeutics

Pathological calcification is a major cause of cardiovascular morbidities primarily in population with chronic kidney disease (CKD), end stage renal diseases (ERSD) and metabolic disorders. Investigators have accepted the fact that vascular calcification is not a passive process but a highly complex, cell mediated, active process in patients with cardiovascular disease (CVD) resulting from, metabolic insults of bone fragility, diabetes, hypertension, dyslipidemia and atherosclerosis. Over the years, studies have revealed various mechanisms of vascular calcification like induction of bone formation, apoptosis, alteration in Ca-P balance and loss of inhibition. Novel clinical studies targeting cellular mechanisms of calcification provide promising and potential avenues for drug development. The interventions include phosphate binders, sodium thiosulphate, vitamin K, calcimimetics, vitamin D, bisphosphonates, Myoinositol hexaphosphate (IP6), Denosumab and TNAP inhibitors. Concurrently investigators are also working towards reversing or curing pathological calcification. This review focuses on the relationship of vascular calcification to clinical diseases, regulators and factors causing calcification including genetics which have been identified. At present, there is lack of any significant preventive measures for calcifications and hence this review explores further possibilities for drug development and treatment modalities.

Metrics and the effective computational scientist: process, quality and communication

Recent treatments of computational knowledge worker productivity have focused upon the value the discipline brings to drug discovery using positive anecdotes. While this big picture approach provides important validation of the contributions of these knowledge workers, the impact accounts do not provide the granular detail that can help individuals and teams perform better. I suggest balancing the impact-focus with quantitative measures that can inform the development of scientists. Measuring the quality of work, analyzing and improving processes, and the critical evaluation of communication can provide immediate performance feedback. The introduction of quantitative measures can complement the longer term reporting of impacts on drug discovery. These metric data can document effectiveness trends and can provide a stronger foundation for the impact dialogue.

On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods

Most implicit solvation models require the definition of a molecular surface as the interface that separates the solute in atomic detail from the solvent approximated as a continuous medium. Commonly used surface definitions include the solvent accessible surface (SAS), the solvent excluded surface (SES), and the van der Waals surface. In this study, we present an efficient numerical algorithm to compute the SES and SAS areas to facilitate the applications of finite-difference Poisson-Boltzmann methods in biomolecular simulations. Different from previous numerical approaches, our algorithm is physics-inspired and intimately coupled to the finite-difference Poisson-Boltzmann methods to fully take advantage of its existing data structures. Our analysis shows that the algorithm can achieve very good agreement with the analytical method in the calculation of the SES and SAS areas. Specifically, in our comprehensive test of 1,555 molecules, the average unsigned relative error is 0.27% in the SES area calculations and 1.05% in the SAS area calculations at the grid spacing of 1/2Å. In addition, a systematic correction analysis can be used to improve the accuracy for the coarse-grid SES area calculations, with the average unsigned relative error in the SES areas reduced to 0.13%. These validation studies indicate that the proposed algorithm can be applied to biomolecules over a broad range of sizes and structures. Finally, the numerical algorithm can also be adapted to evaluate the surface integral of either a vector field or a scalar field defined on the molecular surface for additional solvation energetics and force calculations.

A proposal for the revision of molecular boundary typology

Molecular shape is essential in understanding molecular function, and understanding molecular shape requires definition of molecular boundaries. In this paper, we review the conceptual evolution of three molecular boundary types: the van der Waals surface, the Connolly surface, and the Lee-Richards (accessible) surface. Then, we point out the confusion among the names of these surfaces existing in the literature. Since it is desirable to have a well-defined terminology in a discipline, we propose the standard names of the three molecular boundary types and their corresponding volumes in order to maximize consistency among researchers, respect the first individual who defined or computed a surface type, and promote collaboration between biologists and geometers.

A novel approach for identifying the surface atoms of macromolecules

A significant number of atoms lie buried beneath the "molecular surface" of proteins and other biologic macromolecules. Interactions between ligands and these macromolecules are dominated by interactions with the "surface atoms". Although interactions with the "buried" or interior atoms of the macromolecule certainly contribute to the total intermolecular interaction energy, many computer-assisted drug design (CADD) strategies can benefit from the identification of those atoms "on the surface" of proteins and other macromolecules. We have developed a simple, yet novel method to distinguish the surface atoms of macromolecules from the interior atoms which is based on computing the atomic contributions to the solvent-accessible surface (SAS) area. This report describes that method and demonstrates that it compares very favorably with four alternative methods.

The molecular surface package

The Molecular Surface Package is a reimplementation, in C, of a set of earlier FORTRAN programs for computing analytical molecular surfaces, areas, volumes, polyhedral molecular surfaces, and surface curvatures. The software does not do interactive molecular graphics, but it will produce pixel maps of smooth molecular surfaces. The polyhedral molecular surfaces are suited to display on graphics systems with real-time rendering of polyhedra.

New determinations and simplified representations of macromolecular surfaces

Several new methods or improvements of older algorithms determining the different pieces of molecular surface are presented. Their improvement in time and their complexity are discussed. Only the indexes of the atoms on which the pieces are relying are, in fact, determined, since their explicit representation from these numbers varies according to the 3D capabilities of the graphic workstation (dots, grid, etc.), and this generation is not C.P.U. consuming. To have a simplified representation of the surface of macromolecules, a polyhedron with planar triangular faces is then introduced: Each concave triangular surface piece is replaced with planar triangles relying on its three atomic centers, while saddle-shaped rectangles and convex pieces are wholly ignored. A minimal data structure of the polyhedron is then proposed, which contains only topological informations, since no coordinates have been generated. If the atomic radius is then considered to be constant (independent of atomic type), the surface of a set of N points is now defined by the choice of a subset with a topology. This choice is controlled by a parameter of rugosity (the atomic radius). Contrary to Voronoi polyhedrons partition, which gives a topology for a set of N points, our approach gives a topology only for the exterior points of this set. A few applications of this very simple definition of molecular surface are then discussed: the 3D interactive manipulation of macromolecules, the steric intermolecular recognition, and the determination of local and global properties of the surface.

A new tool for the qualitative and quantitative analysis of protein surfaces using B-spline and density of surface neighborhood

To improve the qualitative and quantitative analysis of surfaces of protein, two new methods are proposed: one that smoothes the MS surface of Connolly with B-spline smoothing functions to highlight the significant features of the surface, and one that computes the density of surface neighborhood to allow quantitative comparison.