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Does Surface Conservation Yield? Application to Data-Driven 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
Open access Jul 2026

Integrating AlphaFold2 with physics-based ensemble docking for high-efficiency nanobody discovery

A computational framework that progressed from next-generation sequencing (NGS)derived candidate nanobody sequences to predicted structures using AlphaFold2, and prioritized nanobodies based on predicted binding energy scores supported the practical utility of the framework for enriching functional nanobodies from expe...

Yinghao Guo, Renfang Guan, Lunde Jin et al. · 0 citations
Open access Jul 2026

COACH-D 2.0: A Server for Template-based Modeling of Protein-ligand Interactions.

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 p...

Xiao-Yu An, Hong Wei, Wenkai Wang et al. · 0 citations
Open access Aug 2026

HDOCK-Multimer: integrating docking and combinatorial assembly for structure prediction of large protein complexes

Deep learning methods, such as AlphaFold and RosettaFold, achieve high accuracy in protein structure prediction. However, predicting the structure of large protein complexes remains challenging due to their large size and intricate multi-chain interactions. Docking-based methods can handle large proteins, but are limit...

Xuan Yao, Yifan Ya, Hao Li et al. · 0 citations
Open access Aug 2026

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...

P. Panda · 0 citations
Open access Aug 2026

FlexAutoDock: A Flexible Platform for Automated Molecular Docking and Virtual Screening of Natural and Synthetic Compounds

FlexAutoDock is an automated cloud-based molecular docking platform that provides a unified environment for protein-ligand docking and large-scale virtual screening, providing researchers with an accessible computational resource for accelerating early-stage drug discovery.

Md. Feroj Ahmed, M. Faysal, Khalid Muntasir Sawad et al. · 0 citations

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