Related papers: ResAtom System: Protein and Ligand Affinity Predic…

Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…

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…

Large Artificial Neural Network (ANN) models have demonstrated success in various domains, including general text and image generation, drug discovery, and protein-RNA (ribonucleic acid) binding tasks. However, these models typically demand…

Protein-ligand interactions (PLIs) are fundamental to biochemical research and their identification is crucial for estimating biophysical and biochemical properties for rational therapeutic design. Currently, experimental characterization…

The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact…

A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design.…

The deficiency of segmentation labels is one of the main obstacles to semantic segmentation in the wild. To alleviate this issue, we present a novel framework that generates segmentation labels of images given their image-level class…

We propose HydraScreen, a deep-learning approach that aims to provide a framework for more robust machine-learning-accelerated drug discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network, designed for the…

Computational docking is the core process of computer-aided drug design; it aims at predicting the best orientation and conformation of a small drug molecule when bound to a target large protein receptor. The docking quality is typically…

DNA-binding proteins are a class of proteins which have a specific or general affinity to DNA and include three important components: transcription factors; nucleases, and histones. DNA-binding proteins also perform important roles in many…

Despite achieving state-of-the-art performance, deep learning methods generally require a large amount of labeled data during training and may suffer from overfitting when the sample size is small. To ensure good generalizability of deep…

Accurately predicting drug-target binding affinity (DTA) in silico is a key task in drug discovery. Most of the conventional DTA prediction methods are simulation-based, which rely heavily on domain knowledge or the assumption of having the…

Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on…

In this study, we expand upon the FLIP benchmark-designed for evaluating protein fitness prediction models in small, specialized prediction tasks-by assessing the performance of state-of-the-art large protein language models, including…

In this paper, we propose a new first-order gradient-based algorithm to train deep neural networks. We first introduce the sign operation of stochastic gradients (as in sign-based methods, e.g., SIGN-SGD) into ADAM, which is called as…

Identifying novel drug-target interactions (DTI) is a critical and rate limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, we show that state-of-the-art models fail to…

The key to successful drug design lies in the correct comprehension of protein-ligand interactions. Within the current knowledge paragm, these interactions can be described from both thermodynamic and kinetic perspectives. In recent years,…

Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…

The computational prediction of a protein structure from its sequence generally relies on a method to assess the quality of protein models. Most assessment methods rank candidate models using heavily engineered structural features, defined…

In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…