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Register a new userAn Introduction to Biomolecular Simulations and Docking
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The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given biomolecule also samples (and is sampled by) a rapidly fluctuating local environment comprised of other biopolymers, small molecules, water, ions, etc. that diffuse to within a few nanometers, leading to inter-molecular contacts that stitch together large supramolecular assemblies. Indeed, all biological systems can be viewed as dynamic networks of molecular interactions. As a complement to experimentation, molecular simulation offers a uniquely powerful approach to analyze biomolecular structure, mechanism, and dynamics; this is possible because the molecular contacts that define a complicated biomolecular system are governed by the same physical principles (forces, energetics) that characterize individual small molecules, and these simpler systems are relatively well-understood. With modern algorithms and computing capabilities, simulations are now an indispensable tool for examining biomolecular assemblies in atomic detail, from the conformational motion in an individual protein to the diffusional dynamics and inter-molecular collisions in the early stages of formation of cellular-scale assemblies such as the ribosome. This text introduces the physicochemical foundations of molecular simulations and docking, largely from the perspective of biomolecular interactions.
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The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining p$K_a$ values, and an improved web-based visualization tool for viewing electrostatics.
Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to parallelization to novel uses of hardware. Special focus is placed on classifying algorithms -- most of which are underpinned by a few key ideas -- in order to understand their fundamental strengths and limitations. Although algorithms have proliferated, progress resulting from novel hardware use appears to be more clear-cut than from algorithms alone, partly due to the lack of widely used sampling measures.
One need only compare the number of three-dimensional molecular illustrations in the first (1990) and third (2004) editions of Voet & Voets Biochemistry in order to appreciate this fields profound communicative value in modern biological sciences -- ranging from medicine, physiology, and cell biology, to pharmaceutical chemistry and drug design, to structural and computational biology. The cliche about a picture being worth a thousand words is quite poignant here: The information content of an effectively-constructed piece of molecular graphics can be immense. Because biological function arises from structure, it is difficult to overemphasize the utility of visualization and graphics in molding our current understanding of the molecular nature of biological systems. Nevertheless, creating effective molecular graphics is not easy -- neither conceptually, nor in terms of effort required. The present collection of Rules is meant as a guide for those embarking upon their first molecular illustrations.
Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a new method for quantifying this uncertainty in implicit solvation calculations of small molecules using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many more types of atomic charges; therefore, construction of surrogate models for the charge parameter space requires compressed sensing combined with an iterative rotation method to enhance problem sparsity. We demonstrate the application of the method by presenting results for the uncertainties in small molecule solvation energies based on these approaches. The method presented in this paper is a promising approach for efficiently quantifying uncertainty in a wide range of force field parameterization problems, including those beyond continuum solvation calculations.The intent of this study is to provide a way for developers of implicit solvent model parameter sets to understand the sensitivity of their target properties (solvation energy) on underlying choices for solute radius and charge parameters.
The present Health Crisis tests the response of modern science and medicine to finding treatment for a new COVID-19 disease. The presentation on the world stage of antivirals such as remdesivir, obeys to the continuous investigation of biologically active molecules with multiple theoretical, computational and experimental tools. Diseases such as COVID:19 remind us that research into active ingredients for therapeutic purposes should cover all available sources, such as plants. In the present work, in silico tools, specifically docking study, were used to evaluate the binding and inhibition capacity of an antiviral such as remdesivir on the NSP-12 protein of SARS-CoV, a polymerase that is key in the replication of the SARS-COV virus. The results are then compared with a docking analysis of two natural products (Alpha-Bisabolol and betalain) with SARS-CoV protein, in order to find more candidates for COVID-19 virus replication inhibitors. in addition to increasing studies that help explain the specific mechanisms of the SARs-CoV-2 virus, remembering that we will have to live with the virus for an indefinite time from now on. Finally, natural products such as betalains may have inhibitory effects of a small order but in conjunction with other synergistic active ingredients they may increase their inhibition effect on NSP-12 protein of SARS-CoV.
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