144 related articles for article (PubMed ID: 28720122)
1. Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints.
Liu J; Su M; Liu Z; Li J; Li Y; Wang R
BMC Bioinformatics; 2017 Jul; 18(1):343. PubMed ID: 28720122
[TBL] [Abstract][Full Text] [Related]
2. Iterative Knowledge-Based Scoring Function for Protein-Ligand Interactions by Considering Binding Affinity Information.
Zhao X; Li H; Zhang K; Huang SY
J Phys Chem B; 2023 Oct; 127(42):9021-9034. PubMed ID: 37822259
[TBL] [Abstract][Full Text] [Related]
3. Exploring Scoring Function Space: Developing Computational Models for Drug Discovery.
Bitencourt-Ferreira G; Villarreal MA; Quiroga R; Biziukova N; Poroikov V; Tarasova O; de Azevedo Junior WF
Curr Med Chem; 2024; 31(17):2361-2377. PubMed ID: 36944627
[TBL] [Abstract][Full Text] [Related]
4. Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks.
Jiang H; Fan M; Wang J; Sarma A; Mohanty S; Dokholyan NV; Mahdavi M; Kandemir MT
J Chem Inf Model; 2020 Oct; 60(10):4594-4602. PubMed ID: 33100014
[TBL] [Abstract][Full Text] [Related]
5. Protein-Ligand Scoring with Convolutional Neural Networks.
Ragoza M; Hochuli J; Idrobo E; Sunseri J; Koes DR
J Chem Inf Model; 2017 Apr; 57(4):942-957. PubMed ID: 28368587
[TBL] [Abstract][Full Text] [Related]
6. The scoring of poses in protein-protein docking: current capabilities and future directions.
Moal IH; Torchala M; Bates PA; Fernández-Recio J
BMC Bioinformatics; 2013 Oct; 14():286. PubMed ID: 24079540
[TBL] [Abstract][Full Text] [Related]
7. Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.
Huang SY; Grinter SZ; Zou X
Phys Chem Chem Phys; 2010 Oct; 12(40):12899-908. PubMed ID: 20730182
[TBL] [Abstract][Full Text] [Related]
8. Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery.
Li Z; Huang R; Xia M; Patterson TA; Hong H
Biomolecules; 2024 Jan; 14(1):. PubMed ID: 38254672
[TBL] [Abstract][Full Text] [Related]
9. Ligand placement based on prior structures: the guided ligand-replacement method.
Klei HE; Moriarty NW; Echols N; Terwilliger TC; Baldwin ET; Pokross M; Posy S; Adams PD
Acta Crystallogr D Biol Crystallogr; 2014 Jan; 70(Pt 1):134-43. PubMed ID: 24419386
[TBL] [Abstract][Full Text] [Related]
10. MCCS, a novel characterization method for protein-ligand complex.
Chen M; Feng Z; Wang S; Lin W; Xie XQ
Brief Bioinform; 2021 Jul; 22(4):. PubMed ID: 33051641
[TBL] [Abstract][Full Text] [Related]
11. Expanding the conformational selection paradigm in protein-ligand docking.
Kuzu G; Keskin O; Gursoy A; Nussinov R
Methods Mol Biol; 2012; 819():59-74. PubMed ID: 22183530
[TBL] [Abstract][Full Text] [Related]
12. AffinityVAE: A multi-objective model for protein-ligand affinity prediction and drug design.
Wang M; Li W; Yu X; Luo Y; Han K; Wang C; Jin Q
Comput Biol Chem; 2023 Dec; 107():107971. PubMed ID: 37852036
[TBL] [Abstract][Full Text] [Related]
13. CLAffinity: A Software Tool for Identification of Optimum Ligand Affinity for Competition-Based Primary Screens.
Shave S; Pham NT; Auer M
J Chem Inf Model; 2022 May; 62(10):2264-2268. PubMed ID: 35442032
[TBL] [Abstract][Full Text] [Related]
14. Predicting Affinity Through Homology (PATH): Interpretable Binding Affinity Prediction with Persistent Homology.
Long Y; Donald BR
bioRxiv; 2023 Nov; ():. PubMed ID: 38014181
[TBL] [Abstract][Full Text] [Related]
15. Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity.
Yan Z; Wang J
PLoS One; 2013; 8(9):e74443. PubMed ID: 24098651
[TBL] [Abstract][Full Text] [Related]
16. Decision tree-based identification of important molecular fragments for protein-ligand binding.
Li B; Wang Y; Yin Z; Xu L; Xie L; Xu X
Chem Biol Drug Des; 2024 Jan; 103(1):e14427. PubMed ID: 38230776
[TBL] [Abstract][Full Text] [Related]
17. KGDiff: towards explainable target-aware molecule generation with knowledge guidance.
Qian H; Huang W; Tu S; Xu L
Brief Bioinform; 2023 Nov; 25(1):. PubMed ID: 38040493
[TBL] [Abstract][Full Text] [Related]
18. Functional group based Ligand binding affinity scoring function at atomic environmental level.
Varadwaj PK; Lahiri T
Bioinformation; 2009; 3(6):268-74. PubMed ID: 19255647
[TBL] [Abstract][Full Text] [Related]
19. Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions.
Koehl A; Jagota M; Erdmann-Pham DD; Fung A; Song YS
Pac Symp Biocomput; 2022; 27():22-33. PubMed ID: 34890133
[TBL] [Abstract][Full Text] [Related]
20. 3D molecular generative framework for interaction-guided drug design.
Zhung W; Kim H; Kim WY
Nat Commun; 2024 Mar; 15(1):2688. PubMed ID: 38538598
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]