Structural similarity
View article
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules Open
SwissTargetPrediction is a web tool, on-line since 2014, that aims to predict the most probable protein targets of small molecules. Predictions are based on the similarity principle, through reverse screening. Here, we describe the 2019 ve…
View article
<i>struc2vec</i> Open
Structural identity is a concept of symmetry in which network nodes are\nidentified according to the network structure and their relationship to other\nnodes. Structural identity has been studied in theory and practice over the\npast decad…
View article
METLIN: A Technology Platform for Identifying Knowns and Unknowns Open
METLIN originated as a database to characterize known metabolites and has since expanded into a technology platform for the identification of known and unknown metabolites and other chemical entities. Through this effort it has become a co…
View article
Multiscale structural similarity for image quality assessment Open
The structural similarity image quality paradigm is based on the assumption that the human visual system is highly adapted for extracting structural information from the scene, and therefore a measure of structural similarity can provide a…
View article
Structure analysis of the receptor binding of 2019-nCoV Open
2019-nCoV is a newly identified coronavirus with high similarity to SARS-CoV. We performed a structural analysis of the receptor binding domain (RBD) of spike glycoprotein responsible for entry of coronaviruses into host cells. The RBDs fr…
View article
GPCRdb in 2018: adding GPCR structure models and ligands Open
G protein-coupled receptors are the most abundant mediators of both human signalling processes and therapeutic effects. Herein, we report GPCRome-wide homology models of unprecedented quality, and roughly 150 000 GPCR ligands with data on …
View article
Antimicrobial Peptides from Plants Open
Plant antimicrobial peptides (AMPs) have evolved differently from AMPs from other life forms. They are generally rich in cysteine residues which form multiple disulfides. In turn, the disulfides cross-braced plant AMPs as cystine-rich pept…
View article
Clustering predicted structures at the scale of the known protein universe Open
Proteins are key to all cellular processes and their structure is important in understanding their function and evolution. Sequence-based predictions of protein structures have increased in accuracy 1 , and over 214 million predicted struc…
View article
An updated structural classification of substrate‐binding proteins Open
Substrate‐binding proteins ( SBP s) play an important role in solute uptake and signal transduction. In 2010, Berntsson et al . classified the 114 organism‐specific SBP structures available at that time and defined six protein clusters, ba…
View article
Large-scale determination of previously unsolved protein structures using evolutionary information Open
The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo …
View article
Glutathione S-Transferases in Cancer Open
In humans, the glutathione S-transferases (GST) protein family is composed of seven members that present remarkable structural similarity and some degree of overlapping functionalities. GST proteins are crucial antioxidant enzymes that reg…
View article
Sars‐CoV‐2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics? Open
The Coronavirus Disease 2019 (COVID‐19) is a new viral infection caused by the severe acute respiratory coronavirus 2 (SARS‐CoV‐2). Genomic analyses have revealed that SARS‐CoV‐2 is related to Pangolin and Bat coronaviruses. In this report…
View article
The Defensins Consist of Two Independent, Convergent Protein Superfamilies Open
© 2016 The Author. The defensin and defensin-like proteins are an extensive group of small, cationic, disulfide-rich proteins found in animals, plants, and fungi and mostly perform roles in host defense. The term defensin was originally us…
View article
The structural impact of DNA mismatches Open
The structure and dynamics of all the transversion and transition mismatches in three different DNA environments have been characterized by molecular dynamics simulations and NMR spectroscopy. We found that the presence of mismatches produ…
View article
Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors Open
Insect odorant receptors (ORs) comprise an enormous protein family that translates environmental chemical signals into neuronal electrical activity. These heptahelical receptors are proposed to function as ligand-gated ion channels and/or …
View article
The modular structure of α/β‐hydrolases Open
The α/β‐hydrolase fold family is highly diverse in sequence, structure and biochemical function. To investigate the sequence–structure–function relationships, the Lipase Engineering Database ( https://led.biocatnet.de ) was updated. Overal…
View article
Structural insight into the role of novel SARS-CoV-2 E protein: A potential target for vaccine development and other therapeutic strategies Open
The outbreak of COVID-19 across the world has posed unprecedented and global challenges on multiple fronts. Most of the vaccine and drug development has focused on the spike proteins and viral RNA-polymerases and main protease for viral re…
View article
Portal Protein: The Orchestrator of Capsid Assembly for the dsDNA Tailed Bacteriophages and Herpesviruses Open
Tailed, double-stranded DNA bacteriophages provide a well-characterized model system for the study of viral assembly, especially for herpesviruses and adenoviruses. A wealth of genetic, structural, and biochemical work has allowed for the …
View article
R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes Open
While the opportunities available for targeting RNA with small molecules have been widely appreciated, the challenges associated with achieving specific RNA recognition in biological systems have hindered progress and prevented many resear…
View article
Prediction of Peptide and Protein Propensity for Amyloid Formation Open
Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can …
View article
Analytical and functional similarity of Amgen biosimilar ABP 215 to bevacizumab Open
ABP 215 is a biosimilar product to bevacizumab. Bevacizumab acts by binding to vascular endothelial growth factor A, inhibiting endothelial cell proliferation and new blood vessel formation, thereby leading to tumor vasculature normalizati…
View article
A chemical–biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives Open
An experimental and computational approach to categorizing UVCBs according to chemical and biological similarities.
View article
Prospects of Structural Similarity Index for Medical Image Analysis Open
An image quality matrix provides a significant principle for objectively observing an image based on an alteration between the original and distorted images. During the past two decades, a novel universal image quality assessment has been …
View article
Classification of Beta-Lactamases and Penicillin Binding Proteins Using Ligand-Centric Network Models Open
β-lactamase mediated antibiotic resistance is an important health issue and the discovery of new β-lactam type antibiotics or β-lactamase inhibitors is an area of intense research. Today, there are about a thousand β-lactamases due to the …
View article
Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens Open
Target identification is one of the most critical steps following cell-based phenotypic chemical screens aimed at identifying compounds with potential uses in cell biology and for developing novel disease therapies. Current in silico targe…
View article
Comparative Analysis of the CDR Loops of Antigen Receptors Open
The adaptive immune system uses two main types of antigen receptors: T-cell receptors (TCRs) and antibodies. While both proteins share a globally similar β-sandwich architecture, TCRs are specialized to recognize peptide antigens in the bi…
View article
Similarity Measure for Molecular Structure: A Brief Review Open
Similarity or distance measures have been used widely to calculate the similarity or dissimilarity between two samples of dataset. Cheminformatics is known as the domain that dealing with chemical information and both similarity and distan…
View article
ConA-Like Lectins: High Similarity Proteins as Models to Study Structure/Biological Activities Relationships Open
Lectins are a widely studied group of proteins capable of specific and reversible binding to carbohydrates. Undoubtedly, the best characterized are those extracted from plants of the Leguminosae family. Inside this group of proteins, those…
View article
Predicting protein targets for drug-like compounds using transcriptomics Open
An expanded chemical space is essential for improved identification of small molecules for emerging therapeutic targets. However, the identification of targets for novel compounds is biased towards the synthesis of known scaffolds that bin…
View article
Structural basis for plant lutein biosynthesis from α-carotene Open
Two cytochrome P450 enzymes, CYP97A3 and CYP97C1, catalyze hydroxylations of the β- and ε-rings of α-carotene to produce lutein. Chirality is introduced at the C-3 atom of both rings, and the reactions are both pro-3 R –stereospecific. We …