Related papers: Two Complementary Methods for Relative Quantificat…
We have developed a web server that implements two complementary methods to quantify the depth of ligand binding site (LBS) in protein-ligand complexes: the "secant plane" (SP) and "tangent sphere" (TS) methods. The protein molecular…
Ligand burial depth is an indicator of protein flexibility, as the extent of receptor conformational change required to bind a ligand in general varies directly with its depth of burial. In a companion paper (Reyes, V.M. 2015a), we report…
Due to increased activity in high-throughput structural genomics efforts around the globe, there has been an accumulation of experimental protein 3D structures lacking functional annotation, thus creating a need for structure-based protein…
We present TerraBind, a foundation model for protein-ligand structure and binding affinity prediction that achieves 26-fold faster inference than state-of-the-art methods while improving affinity prediction accuracy by $\sim$20\%. Current…
Prediction of ligand binding sites of proteins is a fundamental and important task for understanding the function of proteins and screening potential drugs. Most existing methods require experimentally determined protein holo-structures as…
Protein structures represent the key to deciphering biological functions. The more detailed form of similarity among these proteins is sometimes overlooked by the conventional structural comparison methods. In contrast, further advanced…
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational…
There is great interest to develop artificial intelligence-based protein-ligand affinity models due to their immense applications in drug discovery. In this paper, PointNet and PointTransformer, two pointwise multi-layer perceptrons have…
Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used,…
Structural relationships among proteins are important in the study of their evolution as well as in drug design and development. The protein 3D structure has been shown to be effective with respect to classifying proteins. Prior work has…
The recognition of essential proteins not only can help to understand the mechanism of cell operation, but also help to study the mechanism of biological evolution. At present, many scholars have been discovering essential proteins…
The protein-ligand binding affinity (PLA) prediction goal is to predict whether or not the ligand could bind to a protein sequence. Recently, in PLA prediction, deep learning has received much attention. Two steps are involved in deep…
Canonical Polyadic (CP) tensor decomposition is a fundamental technique for analyzing high-dimensional tensor data. While the Alternating Least Squares (ALS) algorithm is widely used for computing CP decomposition due to its simplicity and…
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…
A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is conventionally characterised by the extrinsically determined Ramachandran angles. However, a protein backbone has also two independent intrinsic…
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…
Recent development of high-resolution mass spectrometry (MS) instruments enables chemical cross-linking (XL) to become a high-throughput method for obtaining structural information about proteins. Restraints derived from XL-MS experiments…
The presence of tertiary lymphoid structures (TLSs) on pancreatic pathological images is an important prognostic indicator of pancreatic tumors. Therefore, TLSs detection on pancreatic pathological images plays a crucial role in diagnosis…
Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional…
In this paper, we present a decision level fused local Morphological Pattern Spectrum(PS) and Local Binary Pattern (LBP) approach for an efficient shape representation and classification. This method makes use of Earth Movers Distance(EMD)…