Energy Function Of Neural Network Research Articles

De novo design of cavity-containing proteins with a backbone-centered neural network energy function

The design of small-molecule-binding proteins requires protein backbones that contain cavities. Previous design efforts were based on naturally occurring cavity-containing backbone architectures. Here, we designed diverse cavity-containing backbones without predefined architectures by introducing tailored restraints into the backbone sampling driven by SCUBA (Side Chain-Unknown Backbone Arrangement), a neural network statistical energy function. For 521 out of 5816 designs, the root-mean-square deviations (RMSDs) of the Cα atoms for the AlphaFold2-predicted structures and our designed structures are within 2.0Å. We experimentally tested 10 designed proteins and determined the crystal structures of two of them. One closely agrees with the designed model, while the other forms a domain-swapped dimer, where the partial structures are in agreement with the designed structures. Our results indicate that data-driven methods such as SCUBA hold great potential for designing de novo proteins with tailored small-molecule-binding function.

Construction of a Deep Neural Network Energy Function for Protein Physics.

The traditional approach of computational biology consists of calculating molecule properties by using approximate classical potentials. Interactions between atoms are described by an energy function derived from physical principles or fitted to experimental data. Their functional form is usually limited to pairwise interactions between atoms and does not consider complex multibody effects. More recently, neural networks have emerged as an alternative way of describing the interactions between biomolecules. In this approach, the energy function does not have an explicit functional form and is learned bottom-up from simulations at the atomistic or quantum level. In this study, we attempt a top-down approach and use deep learning methods to obtain an energy function by exploiting the large amount of experimental data acquired with years in the field of structural biology. The energy function is represented by a probability density model learned from a large repertoire of building blocks representing local clusters of amino acids paired with their sequence signature. We demonstrated the feasibility of this approach by generating a neural network energy function and testing its validity on several applications such as discriminating decoys, assessing qualities of structural models, sampling structural conformations, and designing new protein sequences. We foresee that, in the future, our methodology could exploit the continuously increasing availability of experimental data and simulations and provide a new method for the parametrization of protein energy functions.

A backbone-centred energy function of neural networks for protein design.

A protein backbone structure is designable if a substantial number of amino acid sequences exist that autonomously fold into it1,2. It has been suggested that the designability of backbones is governed mainly by side chain-independent or side chain type-insensitive molecular interactions3-5, indicating an approach for designing new backbones (ready for amino acid selection) based on continuous sampling and optimization of the backbone-centred energy surface. However, a sufficiently comprehensive and precise energy function has yet to be established for this purpose. Here we show that this goal is met by a statistical model named SCUBA (for Side Chain-Unknown Backbone Arrangement) that uses neural network-form energy terms. These terms are learned with a two-step approach that comprises kernel density estimation followed by neural network training and can analytically represent multidimensional, high-order correlations in known protein structures. We report the crystal structures of nine de novo proteins whose backbones were designed to high precision using SCUBA, four of which have novel, non-natural overall architectures. By eschewing use of fragments from existing protein structures, SCUBA-driven structure design facilitates far-reaching exploration of the designable backbone space, thus extending the novelty and diversity of the proteins amenable to de novo design.

Resource Industry Operation Study: Cooperation, Constraint and Sustainability

The history of Human beings is the one of utilizing natural recourses. With the development of the economic, natural resources industry security risk management increasingly becomes an urgent and international issue. Analyzing the resources industry security under the systematic angle, the resources industry risk control is the complex system. This system is full of energy flowing which can be measured by the entropy. Hopfield neural network is the important neural networks model. The use of Hopfield neural network puts extra systematic directionality restraints on such risk control. It makes the objective function and constraints of resources industry security risk control, in terms of negative entropy, optimized by the Hopfield neural network energy function. Then as an effective try, some conclusions about reducing resources industry security risk also can be got.

Test Pattern Generation of VLSI Circuits Using Hopfield Neural Networks

A new test pattern generation method for the stuck-at faults in VLSI circuits is presented in this paper, the method uses Hopfield neural networks and chaotic simulated annealing. The Hopfield neural network corresponding to a digital circuit is built, the test patterns of faults in digital circuits are produced by computing the optima of the energy function. A chaotic simulated annealing algorithm is designed, which combines the features of chaotic systems and conventional simulated annealing, it is able to take the advantages of the stochastic properties and global search ability of chaotic system. The algorithm is used to compute the optima of the energy function of neural networks in order to produce the test patterns of faults. Experimental results show that the test pattern generation method proposed in this paper can produce the test patterns in short time for both single stuck-at faults and multiple stuck-at faults in digital circuits.

An application of the neural network energy function to machine sequencing

We apply a neural network approach for solving a one-machine sequencing problem to minimize either single- or multi-objectives, namely the total tardiness, total flowtime, maximimum tardiness, maximum flowtime, and number of tardy jobs. We formulate correspondingly nonlinear integer models, for each of which we derive a quadratic energy function, a neural network, and a system of differential equations. Simulation results based on solving the nonlinear differential equations demonstrate that our approach can effectively solve the sequencing problems to optimality in most cases and near optimality in a few cases. The neural network approach can also be implemented on a parallel computing network, resulting in significant runtime savings over the optimization approach.

A new built-in self-repair approach to VLSI memory yield enhancement by using neural-type circuits

It is shown how to represent the objective function of the memory repair problem as a neural-network energy function, and how to exploit the neural network's convergence property for deriving optimal repair solutions. Two algorithms have been developed using a neural network, and their performances are compared with that of the repair most (RM) algorithm. For randomly generated defect patterns, a proposed algorithm with a hill-climbing capability successfully repaired memory arrays in 98% cases, as opposed to RMs 20% cases. It is demonstrated how, by using very small silicon overhead, one can implement this algorithm in hardware within a VLSI chip for built in self repair (BISR) of memory arrays. The proposed auto-repair approach is shown to improve the VLSI chip yield by a significant factor, and it can also improve the life span of the chip by automatically restructuring its memory arrays in the event of sporadic cell failures during the field use.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>