Home

Citation: LI Xu-Dong, HOU Ting-Jun, Xu Xiao-Jie. Comparative Studies of 14 Binding Free Energies Scoring Functions[J]. Acta Physico-Chimica Sinica, ;2005, 21(05): 504-507. doi: 10.3866/PKU.WHXB20050509 shu

Comparative Studies of 14 Binding Free Energies Scoring Functions

1.
College of Chemistry and Molecular Engineering, Peking University, Beijing 100871

Received Date: 28 September 2004
Available Online: 15 May 2005

Fourteen scoring functions (Ligscore1, Ligscore2, Plp1, Plp2, Jain, Pmf, Ludi1, Ludi2, Ludi3, D-score, Pmf-score, G-score, Chemscore and Xscore) have been compared on a testing set containing 230 protein-ligand complexes to evaluate their abilities to reproduce experimentally determined structures and binding free energies after conformational sampling by the program Ligandfit. When applied to predict the binding free energy of the 230 protein-ligand complexes, Plp1, Plp2, G-score, Pmf and Xscore can give linear correlation coefficients over 0.50 between experimental determined and computed values. When employed to identify the experimentally observed conformation, if using root-mean-square deviation(rmsd)≤0.20 nm as the criterion, Ligscore1, Ligscore2, Plp1, Plp2 and Xscore can gain success rate larger than 70%. Combining any two or three of the 14 scoring functions into a consensus scoring function further improves the success rate to 80%. The results suggest that Xscore, plp1 and plp2 are more practicable than others in docking and scoring.
- Binding free energy; Molecular docking; Scoring function; Consensus scoring function
1. [1]
  Na Li , Limin Shao . Deduction of the General Formula of the Inverse Function of the Titration Curve. University Chemistry, 2025, 40(3): 390-401. doi: 10.12461/PKU.DXHX202409134
2. [2]
  Jing Wang , Pingping Li , Yuehui Wang , Yifan Xiu , Bingqian Zhang , Shuwen Wang , Hongtao Gao . Treatment and Discharge Evaluation of Phosphorus-Containing Wastewater. University Chemistry, 2024, 39(5): 52-62. doi: 10.3866/PKU.DXHX202309097
3. [3]
  Ruilin Han , Xiaoqi Yan . Comparison of Multiple Function Methods for Fitting Surface Tension and Concentration Curves. University Chemistry, 2024, 39(7): 381-385. doi: 10.3866/PKU.DXHX202311023
4. [4]
  Liuchuang Zhao , Wenbo Chen , Leqian Hu . Discussion on Improvement of Teaching Contents about Common Evaluation Parameters in Analytical Chemistry. University Chemistry, 2024, 39(2): 379-391. doi: 10.3866/PKU.DXHX202308079
5. [5]
  Jianmin Hao , Ruifeng Wu , Ying Wang , Yijia Bai , Xuechuan Gao , Yuying Du . Reform and Practice of Physical Chemistry Course Based on Enhanced Process Assessment and Evaluation. University Chemistry, 2024, 39(8): 78-83. doi: 10.3866/PKU.DXHX202311103
6. [6]
  Shuyong Zhang , Wenfeng Jiang , Changsheng Lu , Genrong Qiang , Yongmei Liu , Xiangyang Tang , Dongcheng Liu , Lili Zhang . Suggestions on Construction and Evaluation Standards for First-Class Chemical Experiment Teaching. University Chemistry, 2025, 40(5): 9-14. doi: 10.12461/PKU.DXHX202502114
7. [7]
  Honglian Liang , Xiaozhe Kuang , Fuping Wang , Yu Chen . Exploration and Practice of Integrating Ideological and Political Education into Physical Chemistry: a Case on Surface Tension and Gibbs Free Energy. University Chemistry, 2024, 39(10): 433-440. doi: 10.12461/PKU.DXHX202405073
8. [8]
  Xintian Xie , Sicong Ma , Yefei Li , Cheng Shang , Zhipan Liu . Application of Machine Learning Potential-based Theoretical Simulations in Undergraduate Teaching Laboratory Course Design. University Chemistry, 2025, 40(3): 140-147. doi: 10.12461/PKU.DXHX202405164
9. [9]
  Bingliang Li , Yuying Han , Dianyang Li , Dandan Liu , Wenbin Shang . One-Step Synthesis of Benorilate Guided by Green Chemistry Principles and in vivo Dynamic Evaluation. University Chemistry, 2024, 39(6): 342-349. doi: 10.3866/PKU.DXHX202311070
10. [10]
  Ruming Yuan , Pingping Wu , Laiying Zhang , Xiaoming Xu , Gang Fu . Patriotic Devotion, Upholding Integrity and Innovation, Wholeheartedly Nurturing the New: The Ideological and Political Design of the Experiment on Determining the Thermodynamic Functions of Chemical Reactions by Electromotive Force Method. University Chemistry, 2024, 39(4): 125-132. doi: 10.3866/PKU.DXHX202311057
11. [11]
  Fengqiao Bi , Jun Wang , Dongmei Yang . Specialized Experimental Design for Chemistry Majors in the Context of “Dual Carbon”: Taking the Assembly and Performance Evaluation of Zinc-Air Fuel Batteries as an Example. University Chemistry, 2024, 39(4): 198-205. doi: 10.3866/PKU.DXHX202311069
12. [12]
  .
  CCS Chemistry | 超分子活化底物为自由基促进高效选择性光催化氧化
  . CCS Chemistry, 2025, 7(10.31635/ccschem.025.202405229): -.
13. [13]
  Chengyi Xiao , Xiaoli Sun , Chen Zhang , Weiwei Li . An In-Depth Analysis of the Scientific Connotations, Testing Methods, and Applications of Free Volume in Polymer Physics. University Chemistry, 2025, 40(4): 33-45. doi: 10.12461/PKU.DXHX202403069
14. [14]
  Manman Jin , Zhiguo Lv , Qingtao Niu . Teaching Reformation and Case Study for “Chemical Process Development and Design” Based on “Just-in-Time” Dynamic and Accurate Matching Industrial Needs. University Chemistry, 2024, 39(11): 108-116. doi: 10.12461/PKU.DXHX202403030
15. [15]
  Guangming Yang , Yunhui Long . Design and Implementation of Analytical Chemistry Curriculum Based on the Learning Community of Teachers and Students. University Chemistry, 2024, 39(3): 132-137. doi: 10.3866/PKU.DXHX202309089
16. [16]
  Jin Tong , Shuyan Yu . Crystal Engineering for Supramolecular Chirality. University Chemistry, 2024, 39(3): 86-93. doi: 10.3866/PKU.DXHX202308113
17. [17]
  Zehua Zhang , Haitao Yu , Yanyu Qi . 多重共振TADF分子的设计策略. Acta Physico-Chimica Sinica, 2025, 41(1): 2309042-. doi: 10.3866/PKU.WHXB202309042
18. [18]
  Wen-Bing Hu . Systematic Introduction of Polymer Chain Structures. University Chemistry, 2025, 40(4): 15-19. doi: 10.3866/PKU.DXHX202401014
19. [19]
  Yong Shu , Xing Chen , Sai Duan , Rongzhen Liao . How to Determine the Equilibrium Bond Distance of Homonuclear Diatomic Molecules: A Case Study of H₂. University Chemistry, 2024, 39(7): 386-393. doi: 10.3866/PKU.DXHX202310102
20. [20]
  Yuhui Yang , Jintian Luo , Biao Zuo . A Teaching Approach to Polymer Surface and Interface in Undergraduate Polymer Physics Courses. University Chemistry, 2025, 40(4): 126-130. doi: 10.12461/PKU.DXHX202408056

Get Citation

PDF

XML

Metrics

PDF Downloads(3148)
Abstract views(3736)
HTML views(200)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

Address：Zhongguancun North First Street 2,100190 Beijing, PR China Tel: +86-010-82449177-888

DownLoad: Full-Size Img PowerPoint

Return