Related papers: Predicting the real-valued distances between resid…

The GOR program for predicting protein secondary structure is extended to include triple correlation. A score system for a residue pair to be at certain conformation state is derived from the conditional weight matrix describing amino acid…

Generative models are invaluable in many fields of science because of their ability to capture high-dimensional and complicated distributions, such as photo-realistic images, protein structures, and connectomes. How do we evaluate the…

Accurate identification of protein nucleic-acid-binding residues poses a significant challenge with important implications for various biological processes and drug design. Many typical computational methods for protein analysis rely on a…

Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence information remains very challenging. Recently evolutionary coupling (EC) analysis, which predicts contacts by…

The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of residue substitutions from amino acid sequences is also…

Introduction Accurate prediction of protein-protein interactions (PPIs) is crucial for understanding cellular functions and advancing drug development. Existing in-silico methods use direct sequence embeddings from Protein Language Models…

In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing…

MOTIVATION: Proteins fold into complex structures that are crucial for their biological functions. Experimental determination of protein structures is costly and therefore limited to a small fraction of all known proteins. Hence, different…

Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…

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 one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…

Protein structure reconstruction from Nuclear Magnetic Resonance (NMR) experiments largely relies on computational algorithms. Recently, some effective low-rank matrix completion (MC) methods, such as ASD and ScaledASD, have been…

Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process. Currently, there is a notable shift towards machine learning (ML) methodologies to aid such procedures. Deep learning has…

Learning from 3D protein structures has gained wide interest in protein modeling and structural bioinformatics. Unfortunately, the number of available structures is orders of magnitude lower than the training data sizes commonly used in…

This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence.…

Contact-assisted protein folding has made very good progress, but two challenges remain. One is accurate contact prediction for proteins lack of many sequence homologs and the other is that time-consuming folding simulation is often needed…

Action recognition is a fundamental problem in computer vision with a lot of potential applications such as video surveillance, human computer interaction, and robot learning. Given pre-segmented videos, the task is to recognize actions…

Interactions between proteins are hard to decipher. Protein-protein interactions are difficult problem to address because they are not based on differences in charge type like protein-DNA or protein-lipid interactions. In this manuscript we…

Residual connections remain ubiquitous in modern neural network architectures nearly a decade after their introduction. Their widespread adoption is often credited to their dramatically improved trainability: residual networks train faster,…

Understanding protein-metal interactions is central to structural biology, with metal ions being vital for catalysis, stability, and signal transduction. Predicting metal-binding residues and metal types remains challenging due to the…