A model binding site for testing scoring functions in molecular docking.

By Binqing Wei, W. Baase, L. Weaver, B. Matthews, Brian K. Shoichet. 2002

214 citations recorded by the source corpus.

Subfields: Electrical and Electronic Engineering, Molecular Biology, Spectroscopy

How researchers see this paper

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

In Electrical and Electronic Engineering

1. John J. Irwin
2. Brian K. Shoichet

In Molecular Biology

1. Shengyou Huang
2. John J. Irwin
3. Brian K. Shoichet
4. Xiaoqin Zou
5. Teague Sterling
6. Ryan G. Coleman
7. Michael Carchia
8. Trent E. Balius

In Spectroscopy

1. John J. Irwin
2. Jürgen Bajorath
3. Michael K. Gilson
4. Shengyou Huang
5. Xiaoqin Zou
6. David L. Mobley
7. Brian K. Shoichet

Citations in the corpus

• Predicting binding free energies: Frontiers and benchmarks (2016, background): “This especially occurs for Val111 in the L99A site (90, 81, 56) and Leu118, Val11, and Val103 in L99A/M102Q (130, 131, 48, 12).”
• Ligand Pose and Orientational Sampling in Molecular Docking (2013, methodology): “Whereas previously we have investigated methods to optimize efficiency in sampling orientations [82] or conformations [79, 80, 94] or in their scoring [95] , here we investigated compiler-level optimization and code efficiencies to increase raw speed.”
• Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. (2006, methodology): “35,36 However, the methods in these papers are based on continuum-solvation approaches.”
• Docking and scoring in virtual screening for drug discovery: methods and applications (2004, background): “For example, altered binding sites that emphasize distinct chemical features can be applied to specifically analyse or calibrate electrostatic contributions, hydrophobic interactions or solvation energies of scoring functions, as has been demonstrated in docking studies on structures of mutated T4 l”
• Virtual screening of chemical libraries (2004, background): “Although the docking-derived hits are very different from natural ligands for a given receptor, they often bind at the active site, interacting with conserved receptor groups, as predicted by the docking progra”
• A practical guide to large-scale docking (2021, methodology): “Atomic desolvation energies for ligand atoms are calculated during ligand building using AMSOL 111 and are included in the ligand conformer library.”