142 related articles for article (PubMed ID: 28342242)
1. A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining.
Barradas-Bautista D; Moal IH; Fernández-Recio J
Proteins; 2017 Jul; 85(7):1287-1297. PubMed ID: 28342242
[TBL] [Abstract][Full Text] [Related]
2. CyClus: a fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys.
Omori S; Kitao A
Proteins; 2013 Jun; 81(6):1005-16. PubMed ID: 23344972
[TBL] [Abstract][Full Text] [Related]
3. Structural and energy determinants in protein-RNA docking.
Pérez-Cano L; Romero-Durana M; Fernández-Recio J
Methods; 2017 Apr; 118-119():163-170. PubMed ID: 27816523
[TBL] [Abstract][Full Text] [Related]
4. Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials.
Pérez-Cano L; Solernou A; Pons C; Fernández-Recio J
Pac Symp Biocomput; 2010; ():293-301. PubMed ID: 19908381
[TBL] [Abstract][Full Text] [Related]
5. Performance of ZDOCK and IRAD in CAPRI rounds 28-34.
Vreven T; Pierce BG; Borrman TM; Weng Z
Proteins; 2017 Mar; 85(3):408-416. PubMed ID: 27718275
[TBL] [Abstract][Full Text] [Related]
6. Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1.
Vangone A; Rodrigues JP; Xue LC; van Zundert GC; Geng C; Kurkcuoglu Z; Nellen M; Narasimhan S; Karaca E; van Dijk M; Melquiond AS; Visscher KM; Trellet M; Kastritis PL; Bonvin AM
Proteins; 2017 Mar; 85(3):417-423. PubMed ID: 27802573
[TBL] [Abstract][Full Text] [Related]
7. Refinement of pairwise potentials via logistic regression to score protein-protein interactions.
Tanemura KA; Pei J; Merz KM
Proteins; 2020 Dec; 88(12):1559-1568. PubMed ID: 32729132
[TBL] [Abstract][Full Text] [Related]
8. New additions to the ClusPro server motivated by CAPRI.
Vajda S; Yueh C; Beglov D; Bohnuud T; Mottarella SE; Xia B; Hall DR; Kozakov D
Proteins; 2017 Mar; 85(3):435-444. PubMed ID: 27936493
[TBL] [Abstract][Full Text] [Related]
9. Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions.
Xu X; Qiu L; Yan C; Ma Z; Grinter SZ; Zou X
Proteins; 2017 Mar; 85(3):424-434. PubMed ID: 27802576
[TBL] [Abstract][Full Text] [Related]
10. pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.
Jiménez-García B; Pons C; Fernández-Recio J
Bioinformatics; 2013 Jul; 29(13):1698-9. PubMed ID: 23661696
[TBL] [Abstract][Full Text] [Related]
11. Energy-based graph convolutional networks for scoring protein docking models.
Cao Y; Shen Y
Proteins; 2020 Aug; 88(8):1091-1099. PubMed ID: 32144844
[TBL] [Abstract][Full Text] [Related]
12. GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters.
Park T; Baek M; Lee H; Seok C
J Comput Chem; 2019 Oct; 40(27):2413-2417. PubMed ID: 31173387
[TBL] [Abstract][Full Text] [Related]
13. Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function.
Iwakiri J; Hamada M; Asai K; Kameda T
J Chem Theory Comput; 2016 Sep; 12(9):4688-97. PubMed ID: 27494732
[TBL] [Abstract][Full Text] [Related]
14. Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.
Sarti E; Gladich I; Zamuner S; Correia BE; Laio A
Proteins; 2016 Sep; 84(9):1312-20. PubMed ID: 27253756
[TBL] [Abstract][Full Text] [Related]
15. Target-specific native/decoy pose classifier improves the accuracy of ligand ranking in the CSAR 2013 benchmark.
Fourches D; Politi R; Tropsha A
J Chem Inf Model; 2015 Jan; 55(1):63-71. PubMed ID: 25521713
[TBL] [Abstract][Full Text] [Related]
16. CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys.
Hou Q; Lensink MF; Heringa J; Feenstra KA
PLoS One; 2016; 11(5):e0155251. PubMed ID: 27166787
[TBL] [Abstract][Full Text] [Related]
17. InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information.
Yu J; Vavrusa M; Andreani J; Rey J; Tufféry P; Guerois R
Nucleic Acids Res; 2016 Jul; 44(W1):W542-9. PubMed ID: 27131368
[TBL] [Abstract][Full Text] [Related]
18. HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.
Weng G; Wang E; Wang Z; Liu H; Zhu F; Li D; Hou T
Nucleic Acids Res; 2019 Jul; 47(W1):W322-W330. PubMed ID: 31106357
[TBL] [Abstract][Full Text] [Related]
19. Scoring of protein-protein docking models utilizing predicted interface residues.
Pozzati G; Kundrotas P; Elofsson A
Proteins; 2022 Jul; 90(7):1493-1505. PubMed ID: 35246997
[TBL] [Abstract][Full Text] [Related]
20. Performance and Its Limits in Rigid Body Protein-Protein Docking.
Desta IT; Porter KA; Xia B; Kozakov D; Vajda S
Structure; 2020 Sep; 28(9):1071-1081.e3. PubMed ID: 32649857
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
