ArticleJournal of computational chemistry2013
DOT2: Macromolecular docking with improved biophysical models.
Article in Journal of computational chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Membrane-bound model of the ternary complex between factor VIIa/tissue factor and factor X.Blood advances · 2025Article
- Bioinformatic Resources for Exploring Human-virus Protein-protein Interactions Based on Binding Modes.Genomics, proteomics & bioinformatics · 2024Review
- Software and Databases for Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Design and Prediction of Aptamers Assisted by In Silico Methods.Biomedicines · 2023Review
- Considering both small and large scale motions of vascular endothelial growth factor (VEGF) is crucial for reliably predicting its binding affinities to DNA aptamers.RSC advances · 2021Article
- Advances in integrative structural biology: Towards understanding protein complexes in their cellular context.Computational and structural biotechnology journal · 2021Review
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Methods and Applications of In Silico Aptamer Design and Modeling.International journal of molecular sciences · 2020Review
- In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data.ACS central science · 2019Article
- Rad54 Phosphorylation Promotes Homologous Recombination by Balancing Rad54 Mobility and DNA Binding.Biophysical journal · 2019Article
- Molecular Modeling Applied to Nucleic Acid-Based Molecule Development.Biomolecules · 2018Review
- Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery.Molecules (Basel, Switzerland) · 2018Review
- Improvements to the APBS biomolecular solvation software suite.Protein science : a publication of the Protein Society · 2018Article
- Software for molecular docking: a review.Biophysical reviews · 2017Review
- Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochromeProceedings of the National Academy of Sciences of the United States of America · 2017Article
- Article
- Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2.Journal of the American Chemical Society · 2016Article
- Article
- Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome.eLife · 2016Article
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5 authors.
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Abstract
Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome.
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