Biomolecules

One of the most common mutations in the serine protease inhibitor Kazal type 1 (SPINK1) gene is the N34S variant which is strongly associated with chronic pancreatitis. Although it is assumed that N34S mutation constitutes a high-risk…

In the last decade, machine learning and artificial intelligence applications have received a significant boost in performance and attention in both academic research and industry. The success behind most of the recent state-of-the-art…

Cataract is one of the most prevalent protein aggregation disorders and still the biggest cause of vision loss worldwide. The human lens, in its core region, lacks turnover of any cells or cellular components; it has therefore evolved…

The relationship between sequence variation and phenotype is poorly understood. Here we use metabolomic analysis to elucidate the molecular mechanism underlying the filamentous phenotype of E. coli strains that carry destabilizing mutations…

This article is interested in the origin of the genetic code, it puts forward a scenario of a simultaneous selection of the bases and amino acids and setting up of a correlation between them. Each amino acid is associated with a pair of its…

Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational…

Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…

This article introduces a novel protein structure alignment method (named TALI) based on the protein backbone torsion angle instead of the more traditional distance matrix. Because the structural alignment of the two proteins is based on…

SARS-CoV-2 (COVID-19), a positive single stranded RNA virus, member of corona virus family, is spreading its tentacles across the world due to lack of drugs at present. Being associated with cough, fever, and respiratory distress, this…

Often the development of novel functional peptides is not amenable to high throughput or purely computational screening methods. Peptides must be synthesized one at a time in a process that does not generate large amounts of data. One way…

Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular condensates underlain by liquid-liquid phase separation (LLPS), we conducted multiple-chain simulations of the N-terminal intrinsically…

The dynamics of the structured water molecules in the hydration shell of the DNA double helix is of paramount importance for the understanding of many biological mechanisms. In particular, the vibrational dynamics of a water spine that is…

Less than 1% of protein sequences are structurally and functionally annotated. Natural Language Processing (NLP) community has recently embraced self-supervised learning as a powerful approach to learn representations from unlabeled text,…

Graph neural networks for molecular property prediction are frequently underspecified by data and fail to generalise to new scaffolds at test time. A potential solution is Bayesian learning, which can capture our uncertainty in the model…

The SARS-CoV-2 pandemic has created a global race for a cure. One approach focuses on designing a novel variant of the human angiotensin-converting enzyme 2 (ACE2) that binds more tightly to the SARS-CoV-2 spike protein and diverts it from…

We outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein…

Compound-protein pairs dominate FDA-approved drug-target pairs and the prediction of compound-protein affinity and contact (CPAC) could help accelerate drug discovery. In this study we consider proteins as multi-modal data including 1D…

For fast development of COVID-19, it is only feasible to use drugs (off label use) or approved natural products that are already registered or been assessed for safety in previous human trials. These agents can be quickly assessed in…

Drug combinations play an important role in therapeutics due to its better efficacy and reduced toxicity. Recent approaches have applied machine learning to identify synergistic combinations for cancer, but they are not applicable to new…

Evolution can be broadly described in terms of mutations of the genotype and the subsequent selection of the phenotype. The full enumeration of a given genotype-phenotype (GP) map is therefore a powerful technique in examining evolutionary…