相关论文: A Deterministic Approach to the Protein Design Pro…

The present work provides a new approach to evolve ligand structures which represent possible drug to be docked to the active site of the target protein. The structure is represented as a tree where each non-empty node represents a…

The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…

Proteins are macromolecules responsible for essential functions in almost all living organisms. Designing reasonable proteins with desired functions is crucial. A protein's sequence and structure are strongly correlated and they together…

We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…

Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…

Recent studies have shown competitive performance in protein design that aims to find the amino acid sequence folding into the desired structure. However, most of them disregard the importance of predictive confidence, fail to cover the…

Protein structure prediction has been a grand challenge for over 50 years, owing to its broad scientific and application interests. There are two primary types of modeling algorithms, template-free modeling and template-based modeling. The…

We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…

The formation of correlations due to collisions in an interacting nucleonic system is investigated. Results from one-time kinetic equations are compared with the Kadanoff and Baym two-time equation with collisions included in Born…

Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…

Searching through chemical space is an exceptionally challenging problem because the number of possible molecules grows combinatorially with the number of atoms. Large, autoregressive models trained on databases of chemical compounds have…

A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of twenty single chain proteins. Strikingly, the percentage of successful identification of the nature…

Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…

Application of the principle of energy balance to a rigid indenter in contact with elastic layer on a flat rigid substrate provides a very simple derivation of the detachment criterion which earlier has been obtained by much more…

The interaction between proteins and nucleic acids is crucial for processes that sustain cellular function, including DNA maintenance and the regulation of gene expression and translation. Amino acid mutations in protein-nucleic acid…

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…

Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…

The tasks of designing RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we formulate these problems as continuous optimization and develop…

We study the statistical properties of contact vectors, a construct to characterize a protein's structure. The contact vector of an N-residue protein is a list of N integers n_i, representing the number of residues in contact with residue…

The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…