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Current protein forcefields like the ones seen in CHARMM or Xplor-NIH have many terms that include bonded and non-bonded terms. Yet the forcefields do not take into account the use of hydrogen bonds which are important for secondary…
This paper offers a new authentication algorithm based on image matching of nano-resolution visual identifiers with tree-shaped patterns. The algorithm includes image-to-tree conversion by greedy extraction of the fractal pattern skeleton…
Recent advancements in protein design have leveraged diffusion models to generate structural scaffolds, followed by a process known as protein inverse folding, which involves sequence inference on these scaffolds. However, these…
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…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
We have developed an analytical, ligand-specific and scalable algorithm that detects a "signature" of the 3D binding site of a given ligand in a protein 3D structure. The said signature is a 3D motif in the form of an irregular tetrahedron…
Singular points of a fingerprint image are special locations having high curvature properties. They can play a pivotal role in fingerprint normalization and reliable feature extraction. Accurate and efficient extraction of a singular point…
This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…
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…
Nanopore protein sequencing produces long, noisy ionic current traces in which key molecular phases, such as protein capture and translocation, are embedded. Capture phases mark the successful entry of a protein into the pore and serve as…
Designing protein sequences that fold into a target 3D structure, known as protein inverse folding, is a fundamental challenge in protein engineering. While recent deep learning methods have achieved impressive performance by recovering…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
We present a novel method that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The PRED-TMR algorithm described, refines a standard hydrophobicity analysis with a detection of potential…
Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e.,…
The isolation forest algorithm for outlier detection exploits a simple yet effective observation: if taking some multivariate data and making uniformly random cuts across the feature space recursively, it will take fewer such random cuts…
Molecular building blocks interacting at the nanoscale organize spontaneously into stable mono- layers that display intriguing long-range ordering motifs on the surface of atomic substrates. The patterning process, if appropriately…
As protein therapeutics play an important role in almost all medical fields, numerous studies have been conducted on proteins using artificial intelligence. Artificial intelligence has enabled data driven predictions without the need for…
A device capable of performing real time classification of proteins in a clinical setting would allow for inexpensive and rapid disease diagnosis. One such candidate for this technology are nanopore devices. These devices work by measuring…
Molecular docking is a central method in the computer-based screening of compound libraries as a part of the rational approach to drug design. Although the method has proved its competence in predicting binding modes correctly, its inherent…
Lane detection plays a critical role in the field of autonomous driving. Prevailing methods generally adopt basic concepts (anchors, key points, etc.) from object detection and segmentation tasks, while these approaches require manual…