Biomolecules
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
Single Particle Tracking (SPT) is a powerful class of tools for analyzing the dynamics of individual biological macromolecules moving inside living cells. The acquired data is typically in the form of a sequence of camera images that are…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
In this paper, we investigate potential biases in datasets used to make drug binding predictions using machine learning. We investigate a recently published metric called the Asymmetric Validation Embedding (AVE) bias which is used to…
Traditional approaches to elucidation of protein structures by NMR spectroscopy rely on distance restraints also know as nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR spectroscopy…
Proteins and nucleic acids can spontaneously self-assemble into membraneless droplet-like compartments, both in vitro and in vivo. A key component of these droplets are multi-valent proteins that possess several adhesive domains with…
RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to partition function-based ones that assemble structures using…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
Hydrogenase occupy a central place in the energy metabolism of anaerobic bacteria. Although the structure of mitochondrial complex I is similar to that of hydrogenase, whether it has hydrogen metabolic activity remain unclear. Here, we show…
The phase separation of oppositely-charged polyelectrolytes in solution is of current interest . In this work we study the driving force for polyelectrolyte complexation using molecular dynamics simulations. We calculate the potential of…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning in the directed evolution workflow.…
Abnormal hemoglobins can have major consequences for tissue delivery of oxygen. Correct diagnosis of hemoglobinopathies with altered oxygen affinity requires a determination of hemoglobin oxygen dissociation curve (ODC), which relates the…
Metal nanoclusters (NCs), typically consisting of a few to tens of metal atoms, bridge the gap between organometallic compounds and crystalline metal nanoparticles. As their size approaches the Fermi wavelength of electrons, metal NCs…
Predicting compound-protein affinity is critical for accelerating drug discovery. Recent progress made by machine learning focuses on accuracy but leaves much to be desired for interpretability. Through molecular contacts underlying…
Despite an explosion in the number of experimentally determined, atomically detailed structures of biomolecules, many critical tasks in structural biology remain data-limited. Whether performance in such tasks can be improved by using large…
Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved residue-residue contact prediction, contact-based…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
Phosphate groups are naturally present in starch at C3- or C6-position of the glucose residues and impact the structure of starch granules. Their precise quantification is necessary for understanding starch physicochemical properties and…
Neopetrosia exigua has received great attention in natural product chemistry. The diversity of N. exigua constituents has been demonstrated by the continued discovery of novel bioactive metabolites such as antimicrobial metabolites. In this…