SwarmDock: a server for flexible protein-protein docking
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Summary
A web server that wraps and extends the SwarmDock flexible protein-protein docking algorithm, which generates low energy conformations and returns a ranked list of clustered docking poses and their corresponding structures.
- Type
- article
- Published
- 2013-03-15
- Cited by
- 263
- References
- 7
- Access
- Open access
- OpenAlex
- https://openalex.org/W2140522686
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:206342448
Keywords
Docking (animal), Upload, Computer science, Web server, Macromolecular docking
References
- Designing coarse grained-and atom based-potentials for protein-protein docking
- SwarmDock and the Use of Normal Modes in Protein-Protein Docking
- Docking and scoring protein complexes: CAPRI 3rd Edition
- Detection and refinement of encounter complexes for protein–protein docking: Taking account of macromolecular crowding
- ClusPro: an automated docking and discrimination method for the prediction of protein complexes
- A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding
- Protein-Protein Docking Benchmark Version 4.0
Cited by
- Theoretical and experimental restraints to drive the docking of protein-protein complexes
- Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2
- High-resolution protein-protein docking by global optimization: recent advances and future challenges.
- Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors
- Expanding the frontiers of protein–protein modeling: From docking and scoring to binding affinity predictions and other challenges
- Knowledge of Native Protein-Protein Interfaces Is Sufficient To Construct Predictive Models for the Selection of Binding Candidates
- On the use of knowledge-based potentials for the evaluation of models of protein-protein, protein-DNA, and protein-RNA interactions.
- Probabilistic Approaches to Protein-Protein Docking
- Score_set: A CAPRI benchmark for scoring protein complexes
- A Markov‐chain model description of binding funnels to enhance the ranking of docked solutions
- Structural neighboring property for identifying protein-protein binding sites
- Search strategies and evaluation in protein-protein docking: principles, advances and challenges.
- Identification of Potential Plk1 Targets in a Cell-Cycle Specific Proteome through Structural Dynamics of Kinase and Polo Box-Mediated Interactions
- Intermolecular Contact Potentials for Protein-Protein Interactions Extracted from Binding Free Energy Changes upon Mutation.
- Predicting peptide binding sites on protein surfaces by clustering chemical interactions
- A Viral-Human Interactome Based on Structural Motif-Domain Interactions Captures the Human Infectome
- ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability
- webSDA: a web server to simulate macromolecular diffusional association
- RaTrav: a tool for calculating mean first-passage times on biochemical networks
- Full genome sequences and molecular characterization of tick-borne encephalitis virus strains isolated from human patients.
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