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Somatic mutations in cancer cells affect various genomic elements disrupting important cell functions. In particular, mutations in DNA binding sites recognized by transcription factors can alter regulator binding affinities and expression…
Pathogenic Gram-negative bacteria have developed resistance to antibiotics due to their ability in creating an envelope on the outer layer of lipooligosaccharides (LOS). The cationic phosphoethanolamine (PEA) decoration of LOS lipid A is…
Adaptive therapy is a recent paradigm in cancer treatment aiming at indefinite, safe containment of the disease when cure is judged unattainable. In modeling this approach, inherent limitations arise due to the structure of the vector…
The anti-cancer immune response relies on the bindings between T-cell receptors (TCRs) and antigens, which elicits adaptive immunity to eliminate tumor cells. This ability of the immune system to respond to novel various neoantigens arises…
Reversible covalent kinase inhibitors (RCKIs) are a class of novel kinase inhibitors attracting increasing attention because they simultaneously show the selectivity of covalent kinase inhibitors, yet avoid permanent…
Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or…
Fragment-Based Drug Discovery (FBDD) is a popular approach in early drug development, but designing effective linkers to combine disconnected molecular fragments into chemically and pharmacologically viable candidates remains challenging.…
Drug resistance to HIV-1 Protease involves accumulation of multiple mutations in the protein. Here we investigate the role of these mutations by using molecular dynamics simulations which exploit the influence of the native-state topology…
The current state of cancer therapeutics has been moving away from one-size-fits-all cytotoxic chemotherapy, and towards a more individualized and specific approach involving the targeting of each tumor's genetic vulnerabilities. Different…
Currently, approximately 30% of epileptic patients treated with antiepileptic drugs (AEDs) remain resistant to treatment (known as refractory patients). This project seeks to understand the underlying similarities in refractory patients vs.…
Antibody design methods condition on antigen structure to generate complementarity-determining regions (CDR), yet a systematic evaluation of baseline methods reveals that they largely ignore the antigen input. We identify three failure…
Accurate structural response prediction forms a main driver for structural health monitoring and control applications. This often requires the proposed model to adequately capture the underlying dynamics of complex structural systems. In…
Early identification of sensitive cancer cell lines is essential for accelerating biomarker discovery and elucidating drug mechanism of action. Given the efficiency and low cost of small-scale drug screens relative to extensive omics…
Phagocytosis is the fundamental cellular process by which eukaryotic cells bind and engulf particles by their cell membrane. Particle engulfment involves particle recognition by cell-surface receptors, signaling and remodeling of the actin…
Research on kinase-targeting drugs has made great strides over the last 30 years and is attracting greater attention for the treatment of yet more kinase-related diseases. Currently, 42 kinase drugs have been approved by the FDA, most of…
Uncompetitive antagonists of the N-methyl D-aspartate receptor (NMDAR) have demonstrated therapeutic benefit in the treatment of neurological diseases such as Parkinson's and Alzheimer's, but some also cause dissociative effects that have…
Acquired resistance is one of the major barriers to successful cancer therapy. The development of resistance is commonly attributed to genetic heterogeneity. However, heterogeneity of drug penetration of the tumor microenvironment both on…
The long-term efficacy of targeted therapeutics for cancer treatment can be significantly limited by the type of therapy and development of drug resistance, inter alia. Experimental studies indicate that the factors enhancing acquisition of…
Machine learning and deep learning have gained popularity and achieved immense success in Drug discovery in recent decades. Historically, machine learning and deep learning models were trained on either structural data or chemical…
Accurate prognosis of non-small cell lung cancer (NSCLC) patients undergoing immunotherapy is essential for personalized treatment planning, enabling informed patient decisions, and improving both treatment outcomes and quality of life.…