The flexible data-driven docking method HADDOCK is able to predict many of the specific DNA conformational changes required to assemble the interface(s) and is the first to readily dock multiple molecules simultaneously, pushing the limits of what is currently achievable in the field of protein–DNA docking.
The interface prediction program WHISCY is presented, which combines surface conservation and structural information to predict protein–protein interfaces and demonstrates the potential of using interface predictions to drive protein–protein docking.
S. D. de Vries, A. V. van Dijk, A. M. J. J. Bonvin· 0 citations
It is shown that commonly used modeling approaches, including RNAComposer and AlphaFold3, fail to reliably reproduce aptamer conformations, particularly at the binding sites critical for molecular recognition.
Evaluating modern AMBER-based parametrizations across diverse structural motifs, including aptamers, duplexes, and quadruplex-duplex hybrids, provides critical insights for developing next-generation DNA force fields capable of accurately modeling non-native structures and enabling balanced sampling essential for predicting ligand binding in diverse biological contexts.
G. Bekker, Y. Fukunishi, Junichi Higo et al.· Journal of Chemical Theory a...· 0 citations
Summary Prot2Surf is a software tool designed for the characterization and prediction of protein association to surfaces. In this application note, Prot2Surf was tested using catalytic domains of the lytic polysaccharide monooxygenases (LPMOs), interacting with native surfaces. The results show that the software can efficiently analyze key binding features, including protein–surface distances, distances between catalytically reactive atoms, and the orientation angle between surface chains and the protein. These features are essential for distinguishing productive binding poses in these protein–surface systems and for understanding interaction patterns that provide guidance on protein engineering. Prot2Surf performs these analyses within seconds to a few minutes, providing a fast and accessible framework to post-process and characterize protein-surface encounter complexes. Availability and implementation Prot2Surf, which is written in Fortran90, is documented and freely available as open source on GitHub: https://github.com/TUNNELING-GROUP/Prot2Surf. In order to run Prot2Surf, users should also install the SDA software package which is freely available at https://www.h-its.org/downloads/sda7/.
Abraham Muñiz-Chicharro, Gamze Tanriver, Artur Góra· bioRxiv· 0 citations
COACH-D 2.0 is introduced, a substantially enhanced template-based method for predicting protein-ligand binding sites and features three key advances: integration of multimeric templates from Q-BioLiP into the authors' in-house library, a new multimeric structure processing module enabling binding site prediction for protein complexes, and an efficient template screening strategy that significantly boosts both prediction speed and accuracy.
Xiao-Yu An, Hong Wei, Wenkai Wang et al.· Genomics, Proteomics & Bioin...· 0 citations
An improved force field is developed, derived from its parent, Amber ff24EXP-GA, and its evaluation against Amber ff14SB and other contemporary force fields, such as CHARMM36m, in capturing the empirically determined conformational properties of unfolded systems: short peptides that serve as model systems for IDPs, and longer unfolded proteins.
Athul Suresh, B. Urbanc· 0 citations
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