相关论文: A multi-resolution model to capture both global fl…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at…
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open…
We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that…
Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…
We introduce a simplified protein model where the solvent (water) degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover the thermodynamic phenomenology of proteins over a…
Proteins are made of atoms constantly fluctuating, but can occasionally undergo large-scale changes. Such transitions are of biological interest, linking the structure of a protein to its function with a cell. Atomic-level simulations, such…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use quasi-elastic neutron…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The cornerstone of computational drug design is the calculation of binding affinity between two biological counterparts, especially a chemical compound, i.e., a ligand, and a protein. Predicting the strength of protein-ligand binding with…
Adaptive Molecular Resolution approaches in Molecular Dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Most of the current understanding of structure-property relations at the molecular and the supramolecular scales can be formulated in terms of the stability of and the interactions between a limited number of recurring structural motifs…
Consistency and reliability are crucial for conducting AI research. Many famous research fields, such as object detection, have been compared and validated with solid benchmark frameworks. After AlphaFold2, the protein folding task has…
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…
Freestanding oxide films offer significant potential for integrating exotic quantum functionalities with semiconductor technologies. However, their performance is critically limited by surface roughness and interfacial imperfection caused…
A numerical method is presented to obtain approximate solutions to problems arising from sedimentation models. These processes are widely utilized in minery for recovering water from suspensions coming out of flotation processes. The main…