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This independent research investigates methods to improve the precision of cyclic peptide generation targeting the HIV gp120 trimer using AlphaFold. The study explores proximity-based hotspot mapping at the CD4 binding site, centroid…
Background: In the Nearest-Neighbor Thermodynamic Model, a standard approach for RNA secondary structure prediction, the energy of the multiloops is modeled using a linear entropic penalty governed by three branching parameters. Although…
Drug discovery through virtual screening (VS) has become a popular strategy for identifying hits against protein targets. Alongside VS, molecular design further expands accessible chemical space. Together, these approaches have the…
Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing…
DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a broad set of design frameworks has emerged to accommodate…
Biomolecules exhibit a remarkable property of transforming signals from their environment. This paper presents a communication system design using a light-modulated protein channel: Synthetic Photoisomerizable Azobenzene-regulated K+…
Distance Geometry plays a central role in determining protein structures from Nuclear Magnetic Resonance (NMR) data, a task known as the Molecular Distance Geometry Problem (MDGP). A subclass of this problem, the Discretizable Distance…
The specific region of an antibody responsible for binding to an antigen, known as the paratope, is essential for immune recognition. Accurate identification of this small yet critical region can accelerate the development of therapeutic…
Due to the ever-rising global incidence rate of inflammatory bowel disease (IBD) and the lack of effective clinical treatment drugs, elucidating the detailed pathogenesis, seeking novel targets, and developing promising drugs are the top…
Peptide drugs incorporating non-standard amino acids (NSAAs) offer improved binding affinity and improved pharmacological properties. However, existing peptide design methods are limited to standard amino acids, leaving NSAA-aware design…
Nowadays there is a big spotlight cast on the development of techniques of explainable machine learning. Here we introduce a new computational paradigm based on Group Equivariant Non-Expansive Operators, that can be regarded as the product…
With the advent of diffusion models, new proteins can be generated at an unprecedented rate. The motif scaffolding problem requires steering this generative process to yield proteins with a desirable functional substructure called a motif.…
Data-Independent Acquisition (DIA) was introduced to improve sensitivity to cover all peptides in a range rather than only sampling high-intensity peaks as in Data-Dependent Acquisition (DDA) mass spectrometry. However, it is not very clear…
Recent advances in structure-based protein design have accelerated de novo binder generation, yet interfaces on large domains or spanning multiple domains remain challenging due to high computational cost and declining success with…
Predicting the 3D conformation of small molecules within protein binding sites is a key challenge in drug design. When a crystallized reference ligand (template) is available, it provides geometric priors that can guide 3D pose prediction.…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Reparameterized diffusion models (RDMs) have recently matched autoregressive methods in protein generation, motivating their use for challenging tasks such as designing membrane proteins, which possess interleaved soluble and transmembrane…
Performing cell-free expression (CFE) in tailored microfluidic environments is a powerful tool to investigate the organisation of biosystems from molecular to multicellular scales. While cell-free transcription-translation systems simplify…
The rapid discovery of new chemical compounds is essential for advancing global health and developing treatments. While generative models show promise in creating novel molecules, challenges remain in ensuring the real-world applicability…
Proteins are the workhorse molecules of the cell and perform their biological functions by binding to other molecules through physical contact. Protein function is then regulated through coupling of bindings on the protein (allosteric…