相关论文: A multi-resolution model to capture both global fl…
Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and…
Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
In this article, we apply the binary level set method to the Variational Implicit Solvent Model (VISM), which is a theoretical and computational tool to study biomolecular systems with complex topology. Central in VISM is an effective free…
Simulation techniques based on accurate and efficient representations of potential energy surfaces are urgently needed for the understanding of complex aqueous systems such as solid-liquid interfaces. Here, we present a machine learning…
Recent developments in enhanced sampling methods showed that it is possible to reconstruct ligand unbinding pathways with spatial and temporal resolution inaccessible to experiments. Ideally, such techniques should provide an atomistic…
We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
In this paper, we introduce a new scheme for the efficient numerical treatment of the electronic Schr\"odinger equation for molecules. It is based on the combination of a many-body expansion, which corresponds to the so-called bond order…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
This work investigates multi-resolution methodologies for simulating dimer models. The solvent particles which make up the heat bath interact with the monomers of the dimer either through direct collisions (short-range) or through harmonic…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Super-resolution microscopy has revolutionized the fields of chemistry and biology by resolving features at the molecular level. Such techniques can be either "stochastic," gaining resolution through precise localization of point source…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on…