Related papers: Protein Design by Algorithm
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Numerical optimization of complex systems benefits from the technological development of computing platforms in the last twenty years. Unfortunately, this is still not enough, and a large computational time is still necessary when…
Algorithms have been fundamental to recent global technological advances and, in particular, they have been the cornerstone of technical advances in one field rapidly being applied to another. We argue that algorithms possess fundamentally…
Robots are notoriously difficult to design because of complex interdependencies between their physical structure, sensory and motor layouts, and behavior. Despite this, almost every detail of every robot built to date has been manually…
Machine learning algorithms are everywhere, ranging from simple data analysis and pattern recognition tools used across the sciences to complex systems that achieve super-human performance on various tasks. Ensuring that they are…
Deep learning has transformed protein design, enabling accurate structure prediction, sequence optimization, and de novo protein generation. Advances in single-chain protein structure prediction via AlphaFold2, RoseTTAFold, ESMFold, and…
Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
Quantum computers promise to impact industrial applications, for which quantum chemical calculations are required, by virtue of their high accuracy. This perspective explores the challenges and opportunities of applying quantum computers to…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
Predictive algorithms have a powerful potential to offer benefits in areas as varied as medicine or education. However, these algorithms and the data they use are built by humans, consequently, they can inherit the bias and prejudices…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
Algorithms for continuous optimization problems have a rich history of design and innovation over the past several decades, in which mathematical analysis of their convergence and complexity properties plays a central role. Besides their…
Protein design with desirable properties has been a significant challenge for many decades. Generative artificial intelligence is a promising approach and has achieved great success in various protein generation tasks. Notably, diffusion…
Computer algorithms are written with the intent that when run they perform a useful function. Typically any information obtained is unknown until the algorithm is run. However, if the behavior of an algorithm can be fully described by…
The purpose of this paper is to give an introduction to the field of Schema Theory written by a mathematician and for mathematicians. In particular, we endeavor to to highlight areas of the field which might be of interest to a…
Protein design is a fundamental challenge in biotechnology, aiming to design novel sequences with specific functions within the vast space of possible proteins. Recent advances in deep generative models have enabled function-based protein…
Predicting protein structure from amino acid sequence is one of the most important unsolved problems of molecular biology and biophysics.Not only would a successful prediction algorithm be a tremendous advance in the understanding of the…
Molecule design is a fundamental problem in molecular science and has critical applications in a variety of areas, such as drug discovery, material science, etc. However, due to the large searching space, it is impossible for human experts…
According to some algorithmicists, algorithmics traditionally uses algorithm theory, which stems from mathematics. The growing need for innovative algorithms has caused increasing gaps between theory and practice. Originally, this motivated…