相关论文: High fitness paths can connect proteins with low s…
Protein structures and functions are determined by a contiguous arrangement of amino acid sequences. Designing novel protein sequences and structures with desired geometry and functions is a complex task with large state spaces. Here we…
Deep neural networks such as AlphaFold and RoseTTAFold predict remarkably accurate structures of proteins compared to other algorithmic approaches. It is known that biologically small perturbations in the protein sequence do not lead to…
The idea of this project is to study the protein structure and sequence relationship using the hidden markov model and artificial neural network. In this context we have assumed two hidden markov models. In first model we have taken protein…
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is…
Complex networks encountered in biology are often characterized by significant structural diversity. Whether it be differences in the three-dimensional structure of allosteric proteins, or the variation among the micro-scale structures of…
Emergence of new protein structures has proved difficult to trace in nature and engineer in the laboratory. However, one aspect of structure evolution has proved immensely helpful for determining the three-dimensional structure of proteins…
Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so that the dynamics of the two…
Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its…
Designing novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of functional annotations from wet-lab experiments, previous methods have primarily relied on…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Motivation: The study of diverse enzyme superfamilies can provide important insight into the relationships between protein sequence, structure and function. It is often challenging, however, to discover these relationships across a large…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their members. The typical pipeline to address this task, which we in this paper refer…
Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways. For the trait under evolutionary selection (`fitness'), measured values over all possible combinations of a set of mutations yield…