Calculation of protein-ligand binding affinities.

By Michael K. Gilson, Huan‐Xiang Zhou. Annual Review of Biophysics and Biomolecular Structure, 2007

926 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Physical and Theoretical Chemistry

View Paper: https://www.semanticscholar.org/paper/4ba98d9dd6d6b596af1069e289443bf2ed0d6d81

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In Computational Theory and Mathematics

1. Shengyou Huang
2. Xiaoqin Zou
3. Peng Sang
4. Xing Du
5. Jing Liang
6. Yi Li
7. Xing-lai Ji
8. Shi-Meng Ai

In Molecular Biology

1. Shengyou Huang
2. Xiaoqin Zou
3. Peng Sang
4. Xing Du
5. Jing Liang
6. Yi Li
7. Xing-lai Ji
8. Shi-Meng Ai

In Physical and Theoretical Chemistry

1. Gisbert Schneider
2. Li Xie
3. Shengyou Huang
4. Philip E. Bourne
5. Xiaoqin Zou
6. Lei Xie

Citations in the corpus

• Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, methodology): “current force fields) [15], more efficient sampling techniques, and more accurate solvent models, and the combining of existing methods to make use of the strong points of individual methods [187], could be the main directions to head in.”
• Molecular Docking: Shifting Paradigms in Drug Discovery (2019, background): “Moreover, they might provide inaccurate binding energy estimations [7,23] derived by approximate scoring functions [28,107,108].”
• Advances and Challenges in Protein-Ligand Docking (2010, methodology): “The scoring function is a key element of a protein-ligand docking algorithm, because it directly determines the accuracy of the algorithm [78–82].”
• Virtual screening: an endless staircase? (2010, background): “Furthermore, although in general it might be more valuable to identify ligand chemotypes for which receptor–ligand complex formation is dominated by enthalpy changes rather than entropy changes, improvements are required that allow for a more accurate estimation of both enthalpic and entropic contri”
• Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics (2010, background): “…is more difficult to address as it is based on the inability of current modeling software to treat all kinetic and thermodynamic aspects of binding events such as assessing the effects of water and pH on molecular interactions and incorporating conformational flexibility into calculations (46).”
• Structure-based Systems Biology for Analyzing Off-target Binding (2011, methodology): “The available computational tools used to study quantitative protein-ligand interactions are mostly based on protein-ligand docking and free energy calculations for the protein-ligand complexes [66,67].”
• Protein-Protein and Protein-Ligand Docking (2013, background): “Several reviews on scoring are available in the literature [10-12].”
• Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get” (2009, neutral): “Including such estimates appears to result in improved scoring (Ferrara et al., 2004; Gilson and Zhou, 2007;Shoichet et al., 1999).”