Related papers: Development of antibacterial compounds that block …
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…
Learning how proteins fold will hardly have any impact in the way conventional -- active site centered -- drugs are designed. On the other hand, this knowledge is proving instrumental in defining a new paradigm for the identification of…
Antibiotics are a vital class of drugs closely associated with the prevention and treatment of bacterial infections. Accurate prediction of molecular antimicrobial activity remains a key challenge in the pursuit of novel antibiotic…
Conventional drugs work, as a rule, by inhibiting the enzymatic activity of specific proteins, capping their active site. In this paper we present a model of non- conventional drug design based on the inhibiting effects small peptides…
Antimicrobial resistance is a silent pandemic that is being exacerbated by the uncontrolled use of antibiotics. Since the discovery of penicillin, we have been largely dependent on microbe-derived small molecules to treat bacterial…
Mutational robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of mutational robustness in the budding yeast by genome wide dosage suppressor analysis of 53…
We use fitness graphs, or directed cube graphs, for analyzing evolutionary reversibility. The main application is antimicrobial drug resistance. Reversible drug resistance has been observed both clinically and experimentally. If drug…
In the study of drug function and precision medicine, identifying new drug-microbe associations is crucial. However, current methods isolate association and similarity analysis of drug and microbe, lacking effective inter-view optimization…
Antimicrobial resistance (AMR) poses a mounting global health crisis, requiring rapid and reliable prediction frameworks that capture its complex evolutionary dynamics. Traditional antimicrobial susceptibility testing (AST), while accurate,…
Infections from parasitic nematodes (or roundworms) contribute to a significant disease burden and productivity losses for humans and livestock. The limited number of anthelmintics (or antinematode drugs) available today to treat these…
Understanding how antibiotics inhibit bacteria can help to reduce antibiotic use and hence avoid antimicrobial resistance - yet few theoretical models exist for bacterial growth inhibition by a clinically relevant antibiotic treatment…
Motivation: Antifungal resistance has become an increasing global concern in both clinical and environmental health. Detecting known resistance mutations directly from sequencing reads, in special metagenomic samples, remains a major…
Antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, underscoring the urgent need for new antibiotics. Here we present ApexAmphion, a deep-learning framework for de novo design of antibiotics that…
Antibiotic resistance is a topical problem for both humans and animals and has been the subject of special monitoring for two decades. Several recent studies, including ours, have shown that this phenomenon is accentuated by the transfer of…
A major public health issue is the growing resistance of bacteria to antibiotics. An important part of the needed response is the discovery and development of new antimicrobial strategies. These require the screening of potential new drugs,…
The fast evolution of SARS-CoV-2 and other infectious viruses poses a grand challenge to the rapid response in terms of viral tracking, diagnostics, and design and manufacture of monoclonal antibodies (mAbs) and vaccines, which are both…
New antibiotics are needed to battle growing antibiotic resistance, but the development process from hit, to lead, and ultimately to a useful drug, takes decades. Although progress in molecular property prediction using machine-learning…
Antimicrobial protocols - using substances such as antibiotics or disinfectants - remain the preferred option for preventing the spread of pathogenic bacteria. However, bacteria can develop mechanisms to reduce their antimicrobial…
Drug resistance remains a major problem for the treatment of HIV. Resistance can occur due to mutations that were present before treatment starts or due to mutations that occur during treatment. The relative importance of these two sources…
Predicting how protein mutations affect drug binding remains a major challenge, particularly when the mutations are distal from the binding site. In this study, we introduce a coupled simulation workflow that combines long-time-scale…