Ruler is a local, browser-based tool that uses inter- residue distance measurements to quickly quantify atomic displacements and map changes in internal geometry across ensembles of related protein structures, enabling rapid identification of regions undergoing coordinated motion, local rearrangement, or large-scale conformational change.
A parameter is proposed which can be used as a threshold for acceptance of dynamic domains to enable automatic assignment and has the added advantage of being versatile in that it is applicable to both a pair of structures and an ensemble of conformations.
Steven Hayward· Proteins: Structure, Functio...· 0 citations
Siteomix is an integrated plugin for the PyMOL molecular graphics system that automates the detection of binding pockets via the LIGSITE algorithm, visualizes them as discrete point clouds colored by cavity depth, and performs a two-step alignment combining the rigid iterative closest point (ICP) algorithm with differe...
Kira M. Velieva, E. Skorb, S. Shityakov· Journal of Computer-Aided Mo...· 0 citations
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...
The method successfully recovered the two original protein conformations from a previously published synthetic dataset that traps current refinement methods and produces models for deposited datasets of three separate 14–19 kDa proteins with greatly improved geometry and R-factors.
Spencer K. Passmore, James M. Holton, N. Zatsepin et al.· bioRxiv· 0 citations
Nuclear magnetic resonance (NMR) spectroscopy yields rich residue-level information on biomolecular dynamics and chemical environments, two frontiers for quantitative predictive methods in biochemistry. Decades of data are publicly archived in the Biological Magnetic Resonance Data Bank (BMRB)1, yet in practice, this i...
Gina El Nesr, Hannah K. Wayment-Steele· bioRxiv· 0 citations
Results show that structural information from protein databases can be leveraged to steer AlphaFold2 toward alternative conformations, and AlphaConformers ranked first for modelling subtle conformational changes commonly observed between ligand-bound and unbound states.
Julie Daniel, Lucas Vitoriano De Queiroz Lira, Diego J. Zea· bioRxiv· 0 citations
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