Related papers: Design of Geometric Molecular Bonds
When flat or on a firm mechanical substrate, the atomic composition and atomistic structure of two-dimensional crystals dictate their chemical, electronic, optical, and mechanical properties. These properties change when the two-dimensional…
The diverse combinations of novel building blocks offer a vast design space for hydrogen-boned frameworks (HOFs), rendering it a great promise for gas separation and purification. However, the underlying separation mechanism facilitated by…
There are views prevalent in the noncovalent chemistry literature that i) the O atom in molecules cannot form a chalcogen bond, and ii) if formed, this bond is very weak. We have shown in this study that these views are not necessarily true…
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs…
Peptide-based drugs can bind to protein interaction sites that small molecules often cannot, and are easier to produce than large protein drugs. However, designing effective peptide binders is difficult. A typical peptide has an enormous…
We present a computational scheme for predicting the ligands that bind to a pocket of known structure. It is based on the generation of a general abstract representation of the molecules, which is invariant to rotations, translations and…
Engineering atomic-scale structures allows great manipulation of physical properties and chemical processes for advanced technology. We show that the B atoms deployed at the centers of honeycombs in boron sheets, borophene, behave as nearly…
This paper proposes a new mathematical approach to characterize native protein structures based on the discrete differential geometry of tetrahedron tiles. In the approach, local structure of proteins is classified into finite types…
Understanding the geometry and topology of configuration or conformational spaces of molecules has relevant applications in chemistry and biology such as the proteins folding problem, drug design and the structure activity relationship…
In the domain of geometry and topology optimization, discovering geometries that optimally satisfy specific problem criteria is a complex challenge in both engineering and scientific research. In this work, we propose a new approach for the…
To a system of second order ordinary differential equations (SODE) one can assign a canonical nonlinear connection that describes the geometry of the system. In this work we develop a geometric setting that allows us to assign a canonical…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying "hit" molecules from a large…
In this study, we present a novel molecular fingerprint generation method based on multiparameter persistent homology. This approach reveals the latent structures and relationships within molecular geometry, and detects topological features…
Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…
Straight-forward conformation generation models, which generate 3-D structures directly from input molecular graphs, play an important role in various molecular tasks with machine learning, such as 3D-QSAR and virtual screening in drug…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
A fundamental problem in drug discovery is to design molecules that bind to specific proteins. To tackle this problem using machine learning methods, here we propose a novel and effective framework, known as GraphBP, to generate 3D…
The accurate prediction of protein-ligand binding affinity is important for drug discovery yet remains challenging for multi-domain proteins, where inter-domain dynamics and flexible linkers govern molecular recognition. Current geometric…