Related papers: Protein Chemical Shift Prediction

Introduction: Computational modeling has rapidly advanced over the last decades, especially to predict molecular properties for chemistry, material science and drug design. Recently, machine learning techniques have emerged as a powerful…

The prediction of protein interactions (CPIs) is crucial for the in-silico screening step in drug discovery. Recently, many end-to-end representation learning methods using deep neural networks have achieved significantly better performance…

Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…

Crystal graph neural networks are widely applicable in modeling experimentally synthesized compounds and hypothetical materials with unknown synthesizability. In contrast, structure-agnostic predictive algorithms allow exploring previously…

Many applications of machine learning methods involve an iterative protocol in which data are collected, a model is trained, and then outputs of that model are used to choose what data to consider next. For example, one data-driven approach…

Protein quality assessment (QA) has played an important role in protein structure prediction. We developed a novel single-model quality assessment method - Qprob. Qprob calculates the absolute error for each protein feature value against…

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…

Recent developments in deep learning have made remarkable progress in speeding up the prediction of quantum chemical (QC) properties by removing the need for expensive electronic structure calculations like density functional theory.…

Predicting the structure of interacting chains is crucial for understanding biological systems and developing new drugs. Large-scale pre-trained Protein Language Models (PLMs), such as ESM2, have shown impressive abilities in extracting…

Activity cliff prediction - identifying positions where small structural changes cause large potency shifts - has been a persistent challenge in computational medicinal chemistry. This work focuses on a parsimonious definition: which small…

In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our…

Predicting the binding affinity of protein protein complexes directly from sequence remains a challenging problem, particularly in the absence of reliable structural information. Here I present ProtT Affinity, a sequence only model that…

A cascading system of hierarchical, artificial neural networks (named PRED-CLASS) is presented for the generalized classification of proteins into four distinct classes-transmembrane, fibrous, globular, and mixed-from information solely…

Every molecule ever synthesised can be drawn as a 2D skeletal diagram, yet in modern property prediction this universally available representation has received less focus in favour of molecular graphs, 3D conformers, or billion-parameter…

Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…

Using the perturbation-response scanning (PRS) technique, we study a set of 23 proteins that display a variety of conformational motions upon ligand binding (e.g. shear, hinge, allosteric). In most cases, PRS determines residues that may be…

Virtual screening can accelerate drug discovery by identifying promising candidates for experimental evaluation. Machine learning is a powerful method for screening, as it can learn complex structure-property relationships from experimental…

Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms…

Due to the lack of a method to efficiently represent the multimodal information of a protein, including its structure and sequence information, predicting compound-protein binding affinity (CPA) still suffers from low accuracy when applying…