Rep3D : an algorithm to identify structurally similar motifs

Comparative computational insights into tandem and non-tandem repeats in protein-DNA complexes.

Proteins and DNA interact with each other to carry out various cellular functions. Internal repeats in proteins provides a structural and functional role in establishing these connections. This study offers an in-depth analysis of tandem and non-tandem repeats observed in a non-redundant set of 378 protein-DNA complexes archived in the Protein Data Bank (PDB). The RADAR server was employed to locate these repeats. The role of internal repeats in the structure and function of these proteins were analyzed using PDBsum. Examining the tandem and non-tandem repeats, reveal that the former is shorter, exhibit reduced variability and facilitate structural conservation. In contrast, the latter are more scattered and support many activities, including DNA binding and metal interaction. The root mean square deviation analysis of the observed tandem and non-tandem repeats shows the extent of structural conservation and divergence. Further secondary-structure analysis of the repeat regions were also carried out. Illustrations derived from PDB data demonstrate the distinct interactions of non-tandem and tandem repeats with DNA. The significance of repeat structures in DNA recognition is highlighted.

Protein Structure Characters in the Light of Phylogenetic Systematics

It is concluded that differences in 3Di characters between semaphoronts are not intrinsically a problem, but they do require that the researcher uses the same replicable method on all proteins in the phylogenetic analysis.

DynDom1D_Python: An Open-Source Python tool for the analysis of domain movements in proteins

DynDom1D_Python, an open-source Python implementation based on the original DynDom Fortran program for the analysis of domain movements in proteins, improves on the original standalone version in a number of ways.

ResiRuler: A Toolkit for Visualizing Residue-Residue Distances and Structural Changes in Biomolecular Models

Short Tandem Repeat 3D Structure Database (STR3SD): A Resource for Structural Biology Research of Short Tandem Repeats in Neurodegenerative Disorders

The Short Tandem Repeat 3D Structure Database (STR3SD) is a web-based database that provides a comprehensive resource for structural biology research of short tandem repeats (STRs) in cancers and neurodegenerative diseases. STR3SD contains three-dimensional (3D) structures of STRs surveyed from literature. The data are organized into three main categories, including 3D structures of nucleic acids only, nucleic acids–protein complexes, and nucleic acids–ligand complexes. Under these categories, each entry is annotated with repeat type, molecular type (DNA or RNA), sequence, PDB ID, structural component, ligand name, structural determination method, experimental conditions (temperature, pH, and ion), PubMed ID, and interactive 3D structure view. The database is built on direct literature investigation by human experts and serves as a crucial tool for studying structures and functions of STRs in cancers and neurodegenerative diseases, supporting research on structural polymorphisms and pathogenic mechanisms of STRs, and facilitating drug design targeting STRs for disease therapy.

PandaMap: A Python Package for Comprehensive Visualization of Protein–Ligand Interaction Networks

Protein–ligand interaction diagrams are a routine part of structural and medicinal chemistry, but the tools that produce them tend to force a choice: comprehensive detection with tabular output, publication-quality figures behind a licence, or a scripting environment that assumes expertise. PandaMap (Protein AND ligAnd interaction MAPper) is an open-source Python package that produces a 2D interaction diagram, an interactive 3D viewer, a text report, a machine-readable CSV, and a four-panel graphical summary from a single command. It reads PDB, mmCIF and PDBQT files, detects 15 interaction classes using crystallographically validated distance thresholds, and depends only on NumPy, Matplotlib, BioPython and Requests; RDKit improves the 2D ligand layout when present but is not required. Hydrogen bonds are filtered on the true D–H· · · A angle when the structure contains explicit hydrogens, matching PLIP’s 100◦ criterion on the same evidence, and on distance alone otherwise, with the provenance of each measurement recorded. We benchmarked the package on three complexes chosen for different chemistry: enolase with a phosphonate transition-state analogue (PDB 1ELS), the EGFR kinase with erlotinib (1M17), and aldose reductase with IDD594 (1US0). PandaMap recovers the contacts these structures are known for, including the EGFR hinge hydrogen bond to MET769 and the IDD594 bromine· · · THR113 halogen bond, both at distances identical to PLIP’s. All detection thresholds, scoring weights and the exact commands used are given in the Supplementary Information, and the release carries a regression suite covering each interaction class. PandaMap 4.3.0 is available on PyPI under the MIT licence.