Challenges and advances in computational docking: 2009 in review

By Elizabeth Yuriev, Mark Agostino, Paul A. Ramsland. 2011

323 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Computational Chemistry & Drug Discovery

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Sunghwan Kim
2. Evan E. Bolton
3. Stephen H. Bryant
4. Brian K. Shoichet
5. John J. Irwin
6. Teague Sterling
7. Ryan G. Coleman
8. Michael Carchia

In Molecular Biology

1. Sunghwan Kim
2. Evan E. Bolton
3. Stephen H. Bryant
4. John J. Irwin
5. Brian K. Shoichet
6. Teague Sterling
7. Ryan G. Coleman
8. Michael Carchia

In Computational Chemistry & Drug Discovery

1. Brian K. Shoichet
2. Ryan G. Coleman
3. Teague Sterling
4. Michael Carchia
5. John J. Irwin
6. Elizabeth Yuriev
7. Paul A. Ramsland
8. Adriano Defini Andricopulo

Citations in the corpus

• Molecular Docking and Structure-Based Drug Design Strategies (2015, methodology): “This process is carried out recursively until converging to a solution of minimum energy [23–25].”
• Ligand Pose and Orientational Sampling in Molecular Docking (2013, background): “Molecular docking is widely used to predict protein-ligand complexes[1,2] and to screen large libraries for molecules that will modulate the activity of a biological receptor.”
• Latest developments in molecular docking: 2010–2011 in review (2013, background): “…options of tautomer enumeration in VS. Testing against seven targets from the DUD set, they found that, similar to earlier studies described in, [4] three protocols ((i) all possible tautomeric forms; (ii) all forms with predicted abundance of ≥ 5% in water; and (iii) only the most stable form)…”
• Computational approaches in target identification and drug discovery (2016, methodology): “Depending on the method, there are different considerations of the fl exibility of either the ligand or the protein during the docking process [93].”
• Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls (2015, background): “The issues related to receptor flexibility have been extensively reviewed in literature [28,66,67].”
• Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, background): “Solvation effects are well-known to influence the binding ability of a drug [69, 88].”
• PubChem3D: Diversity of shape (2011, background): “Virtual screening of large chemical databases is now a routine practice in modern drug discovery [1-8].”