Related papers: Protein secondary structure: Entropy, correlations…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
Despite an explosion in the number of experimentally determined, atomically detailed structures of biomolecules, many critical tasks in structural biology remain data-limited. Whether performance in such tasks can be improved by using large…
We use LINUS, a procedure developed by Srinivasan and Rose, to provide a physical interpretation of and to predict the secondary structures of proteins. The secondary structure type at a given site is identified by the largest…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
The 2024 Nobel Prize in Chemistry was awarded in part for protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and 3D structure data. AlphaFold2 and…
An effective model for protein structures is important for the study of protein geometry, which, to a large extent, determine the functions of proteins. There are a number of approaches for modelling; one might focus on the conformation of…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
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…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Numerous experiments demonstrate a high level of promiscuity and structural disorder in organismal proteomes. Here we ask the question what makes a protein promiscuous, i.e., prone to non-specific interactions, and structurally disordered.…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
The Hidden Markov Model (HMM) is one of the most widely used statistical models for sequential data analysis. One of the key reasons for this versatility is the ability of HMM to deal with missing data. However, standard HMM learning…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
The local structure of a protein strongly impacts its function and interactions with other molecules. Therefore, a concise, informative representation of a local protein environment is essential for modeling and designing proteins and…
The length distribution of proteins measured in amino acids follows the CoHSI (Conservation of Hartley-Shannon Information) probability distribution. In previous papers we have verified various predictions of this using the Uniprot database…
The tertiary structure of protein, as well as the local secondary structure organization are fully determined by the angles of the peptidic bound. The backbone dihedral angles not only determine the global fold of the protein, but also the…
Protein-nucleic acid interactions play a very important role in a variety of biological activities. Accurate identification of nucleic acid-binding residues is a critical step in understanding the interaction mechanisms. Although many…
We present a statistical approach to protein structure by introducing a representation of protein folds based on simple observables defined as frequencies of oriented cycles in contact graphs. Motivated by the idea that these cycles may…
Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two…