Computational protein design with backbone plasticity

The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as “scaffolds” onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increase search space but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process

Towards complete configurations using an embedded grid approach

A new approach to simulating transonic flow about transport configurations is briefly outlined. The methods embedded grid scheme provides a high degree of computational resolution coupled with geometric flexibility for future applications to complex shapes. Calculations presented illustrate aspects of transonic transport design including fuselage design, determination of wing control surface deflection effectiveness, and wing design

Research in Geant4 electromagnetic physics design, and its effects on computational performance and quality assurance

The Geant4 toolkit offers a rich variety of electromagnetic physics models; so far the evaluation of this Geant4 domain has been mostly focused on its physics functionality, while the features of its design and their impact on simulation accuracy, computational performance and facilities for verification and validation have not been the object of comparable attention yet, despite the critical role they play in many experimental applications. A new project is in progress to study the application of new design concepts and software techniques in Geant4 electromagnetic physics, and to evaluate how they can improve on the current simulation capabilities. The application of a policy-based class design is investigated as a means to achieve the objective of granular decomposition of processes; this design technique offers various advantages in terms of flexibility of configuration and computational performance. The current Geant4 physics models have been re-implemented according to the new design as a pilot project. The main features of the new design and first results of performance improvement and testing simplification are presented; they are relevant to many Geant4 applications, where computational speed and the containment of resources invested in simulation production and quality assurance play a critical role.Comment: 4 pages, 4 figures and images, to appear in proceedings of the Nuclear Science Symposium and Medical Imaging Conference 2009, Orland

Computational structure‐based drug design: Predicting target flexibility

The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing a competitive advantage in early phases of drug discovery. Medium and small companies with strong focus on computational chemistry are being created, some of them having introduced important leads in drug design pipelines. An important source for this success is the extraordinary development of faster and more efficient techniques for describing flexibility in three‐dimensional structural molecular modeling. At different levels, from docking techniques to atomistic molecular dynamics, conformational sampling between receptor and drug results in improved predictions, such as screening enrichment, discovery of transient cavities, etc. In this review article we perform an extensive analysis of these modeling techniques, dividing them into high and low throughput, and emphasizing in their application to drug design studies. We finalize the review with a section describing our Monte Carlo method, PELE, recently highlighted as an outstanding advance in an international blind competition and industrial benchmarks.We acknowledge the BSC-CRG-IRB Joint Research Program in Computational Biology. This work was supported by a grant from the Spanish Government CTQ2016-79138-R.J.I. acknowledges support from SVP-2014-068797, awarded by the Spanish Government.Peer ReviewedPostprint (author's final draft

Iterative approach to computational enzyme design

A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner, but was flipped relative to the design model. MD analysis of HG-2 led to an additional point mutation, HG-3, that produced a further threefold improvement in activity. This iterative approach to computational enzyme design, including detailed MD and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes

A knowledge-based geometry repair system for robust parametric CAD models

In modern multi-objective design optimization (MDO) an effective geometry engine is becoming an essential tool and its performance has a significant impact on the entire MDO process. Building a parametric geometry requires difficult compromises between the conflicting goals of robustness and flexibility. This article presents a method of improving the robustness of parametric geometry models by capturing and modeling engineering knowledge with a support vector regression surrogate, and deploying it automatically for the search of a more robust design alternative while trying to maintain the original design intent. Design engineers are given the opportunity to choose from a range of optimized designs that balance the ‘health’ of the repaired geometry and the original design intent. The prototype system is tested on a 2D intake design repair example and shows the potential to reduce the reliance on human design experts in the conceptual design phase and improve the stability of the optimization cycle. It also helps speed up the design process by reducing the time and computational power that could be wasted on flawed geometries or frequent human intervention

Totems

In modern multi-objective design optimization (MDO) an effective geometry engine is becoming an essential tool and its performance has a significant impact on the entire MDO process. Building a parametric geometry requires difficult compromises between the conflicting goals of robustness and flexibility. This article presents a method of improving the robustness of parametric geometry models by capturing and modeling engineering knowledge with a support vector regression surrogate, and deploying it automatically for the search of a more robust design alternative while trying to maintain the original design intent. Design engineers are given the opportunity to choose from a range of optimized designs that balance the ‘health’ of the repaired geometry and the original design intent. The prototype system is tested on a 2D intake design repair example and shows the potential to reduce the reliance on human design experts in the conceptual design phase and improve the stability of the optimization cycle. It also helps speed up the design process by reducing the time and computational power that could be wasted on flawed geometries or frequent human intervention

Integrated geometry and grid generation system for complex configurations

A grid generation system was developed that enables grid generation for complex configurations. The system called ICEM/CFD is described and its role in computational fluid dynamics (CFD) applications is presented. The capabilities of the system include full computer aided design (CAD), grid generation on the actual CAD geometry definition using robust surface projection algorithms, interfacing easily with known CAD packages through common file formats for geometry transfer, grid quality evaluation of the volume grid, coupling boundary condition set-up for block faces with grid topology generation, multi-block grid generation with or without point continuity and block to block interface requirement, and generating grid files directly compatible with known flow solvers. The interactive and integrated approach to the problem of computational grid generation not only substantially reduces manpower time but also increases the flexibility of later grid modifications and enhancements which is required in an environment where CFD is integrated into a product design cycle