These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
243 related articles for article (PubMed ID: 31628659)
1. Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies. Macari G; Toti D; Polticelli F J Comput Aided Mol Des; 2019 Oct; 33(10):887-903. PubMed ID: 31628659 [TBL] [Abstract][Full Text] [Related]
3. Prediction of impacts of mutations on protein structure and interactions: SDM, a statistical approach, and mCSM, using machine learning. Pandurangan AP; Blundell TL Protein Sci; 2020 Jan; 29(1):247-257. PubMed ID: 31693276 [TBL] [Abstract][Full Text] [Related]
4. A nearest neighbor algorithm based predictor for the prediction of enzyme-small molecule interaction. Hu LL; He ZS; Shi XH; Kong XY; Li HP; Lu WC Protein Pept Lett; 2012 Jan; 19(1):91-8. PubMed ID: 21919855 [TBL] [Abstract][Full Text] [Related]
5. Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions. Lu J; Hou X; Wang C; Zhang Y J Chem Inf Model; 2019 Nov; 59(11):4540-4549. PubMed ID: 31638801 [TBL] [Abstract][Full Text] [Related]
6. SmoPSI: Analysis and Prediction of Small Molecule Binding Sites Based on Protein Sequence Information. Wang W; Li K; Lv H; Zhang H; Wang S; Huang J Comput Math Methods Med; 2019; 2019():1926156. PubMed ID: 31814842 [TBL] [Abstract][Full Text] [Related]
7. Elucidating Protein-protein Interactions Through Computational Approaches and Designing Small Molecule Inhibitors Against them for Various Diseases. Sarkar S; Gulati K; Kairamkonda M; Mishra A; Poluri KM Curr Top Med Chem; 2018; 18(20):1719-1736. PubMed ID: 30360722 [TBL] [Abstract][Full Text] [Related]
8. Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design. Sotriffer C; Klebe G Farmaco; 2002 Mar; 57(3):243-51. PubMed ID: 11989803 [TBL] [Abstract][Full Text] [Related]
10. Prediction of RNA binding sites in proteins from amino acid sequence. Terribilini M; Lee JH; Yan C; Jernigan RL; Honavar V; Dobbs D RNA; 2006 Aug; 12(8):1450-62. PubMed ID: 16790841 [TBL] [Abstract][Full Text] [Related]
11. Knowledge-based scoring functions in drug design: 3. A two-dimensional knowledge-based hydrogen-bonding potential for the prediction of protein-ligand interactions. Zheng M; Xiong B; Luo C; Li S; Liu X; Shen Q; Li J; Zhu W; Luo X; Jiang H J Chem Inf Model; 2011 Nov; 51(11):2994-3004. PubMed ID: 21999432 [TBL] [Abstract][Full Text] [Related]
12. A critical comparative assessment of predictions of protein-binding sites for biologically relevant organic compounds. Chen K; Mizianty MJ; Gao J; Kurgan L Structure; 2011 May; 19(5):613-21. PubMed ID: 21565696 [TBL] [Abstract][Full Text] [Related]
13. Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration. Lo YT; Wang HW; Pai TW; Tzou WS; Hsu HH; Chang HT BMC Bioinformatics; 2013; 14 Suppl 4(Suppl 4):S4. PubMed ID: 23514235 [TBL] [Abstract][Full Text] [Related]
14. LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction. Kauffman C; Karypis G Bioinformatics; 2009 Dec; 25(23):3099-107. PubMed ID: 19786483 [TBL] [Abstract][Full Text] [Related]
15. A molecular-modeling toolbox aimed at bridging the gap between medicinal chemistry and computational sciences. Eid S; Zalewski A; Smieško M; Ernst B; Vedani A Int J Mol Sci; 2013 Jan; 14(1):684-700. PubMed ID: 23344039 [TBL] [Abstract][Full Text] [Related]
16. Shaping the interaction landscape of bioactive molecules. Gfeller D; Michielin O; Zoete V Bioinformatics; 2013 Dec; 29(23):3073-9. PubMed ID: 24048355 [TBL] [Abstract][Full Text] [Related]
17. Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions. Li Y; Yang J J Chem Inf Model; 2017 Apr; 57(4):1007-1012. PubMed ID: 28358210 [TBL] [Abstract][Full Text] [Related]
18. Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner's Guide. Aldeghi M; Bluck JP; Biggin PC Methods Mol Biol; 2018; 1762():199-232. PubMed ID: 29594774 [TBL] [Abstract][Full Text] [Related]