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AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings.
Eberhardt J, Santos-Martins D, Tillack AF, Forli S. Eberhardt J, et al. J Chem Inf Model. 2021 Aug 23;61(8):3891-3898. doi: 10.1021/acs.jcim.1c00203. Epub 2021 Jul 19. J Chem Inf Model. 2021. PMID: 34278794 Free PMC article.
Here, we describe the implementation of this functionality in AutoDock Vina 1.2.0. Additionally, AutoDock Vina 1.2.0 supports the AutoDock4.2 scoring function, simultaneous docking of multiple ligands, and a batch mode for docking a large number of ligands. . …
Here, we describe the implementation of this functionality in AutoDock Vina 1.2.0. Additionally, AutoDock Vina 1.2.0 supports …
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.
Trott O, Olson AJ. Trott O, et al. J Comput Chem. 2010 Jan 30;31(2):455-61. doi: 10.1002/jcc.21334. J Comput Chem. 2010. PMID: 19499576 Free PMC article.
AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also sig …
AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximatel …
Correlation between Visual Analogue Scale Score and Hospital Anxiety Depression Scale-Depression Score in Patients with Cervical Cancer in the Hospital Vina Cancer, Medan.
Widyastuty A, Effendy E, Amin MM. Widyastuty A, et al. Open Access Maced J Med Sci. 2019 Aug 20;7(16):2634-2637. doi: 10.3889/oamjms.2019.473. eCollection 2019 Aug 30. Open Access Maced J Med Sci. 2019. PMID: 31777622 Free PMC article.
AIM: To determine the correlation between scores of Visual Analogue Scale (VAS) and Hospital Anxiety Depression Scale-Depression (HADS-D) in patients with cervical cancer in Vina Cancer Center Hospital in Medan. ...CONCLUSION: There is a significant correlation betw …
AIM: To determine the correlation between scores of Visual Analogue Scale (VAS) and Hospital Anxiety Depression Scale-Depression (HAD …
[Perfectionism, academic stress and social anxiety in female medical students and the risk for eating disorders].
Mandiola MI, Arancibia M, Elton V, Madrid E, Meza N, Stojanova J, Lutz M, Leyton F. Mandiola MI, et al. Rev Med Chil. 2022 Aug;150(8):1046-1053. doi: 10.4067/S0034-98872022000801046. Rev Med Chil. 2022. PMID: 37358152 Free article. Spanish.
There were significant differences between scores of perfectionism, social anxiety, and academic stress between respondents with and without risk for ED. ...
There were significant differences between scores of perfectionism, social anxiety, and academic stress between respondents with and …
Accelerating AutoDock Vina with GPUs.
Tang S, Chen R, Lin M, Lin Q, Zhu Y, Ding J, Hu H, Ling M, Wu J. Tang S, et al. Molecules. 2022 May 9;27(9):3041. doi: 10.3390/molecules27093041. Molecules. 2022. PMID: 35566391 Free PMC article.
AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best docking power among all the docking tools. ...Due to the seriality characteristic o …
AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark CASF-2016 for comparative assessment of …
3pHLA-score improves structure-based peptide-HLA binding affinity prediction.
Conev A, Devaurs D, Rigo MM, Antunes DA, Kavraki LE. Conev A, et al. Sci Rep. 2022 Jun 24;12(1):10749. doi: 10.1038/s41598-022-14526-x. Sci Rep. 2022. PMID: 35750701 Free PMC article.
For that, we engineer the input features for ML models by decoupling energy contributions at different residue positions in peptides, which leads to our novel per-peptide-position protocol. Using Rosetta's ref2015 scoring function as a baseline we use this protocol to deve …
For that, we engineer the input features for ML models by decoupling energy contributions at different residue positions in peptides, which …
Docking with GemDock.
Bitencourt-Ferreira G, de Azevedo WF Jr. Bitencourt-Ferreira G, et al. Methods Mol Biol. 2019;2053:169-188. doi: 10.1007/978-1-4939-9752-7_11. Methods Mol Biol. 2019. PMID: 31452105
As any docking program, GEMDOCK has two major features to predict the binding of a small-molecule ligand to the binding site of a protein target: the search algorithm and the scoring function to evaluate the generated poses. The GEMDOCK scoring function uses a piece …
As any docking program, GEMDOCK has two major features to predict the binding of a small-molecule ligand to the binding site of a protein ta …
Minimal clinically important difference: The basics.
Salas Apaza JA, Franco JVA, Meza N, Madrid E, Loézar C, Garegnani L. Salas Apaza JA, et al. Medwave. 2021 Apr 7;21(3):e8149. doi: 10.5867/medwave.2021.03.8149. Medwave. 2021. PMID: 35380557 Review. English, Spanish.
The minimal clinically important difference is defined as the smallest difference in score in any domain or outcome of interest that patients can perceive as beneficial. It is a useful concept in several aspects since it links the magnitude of change with treatment decisio …
The minimal clinically important difference is defined as the smallest difference in score in any domain or outcome of interest that …
Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking.
Nivedha AK, Thieker DF, Makeneni S, Hu H, Woods RJ. Nivedha AK, et al. J Chem Theory Comput. 2016 Feb 9;12(2):892-901. doi: 10.1021/acs.jctc.5b00834. Epub 2016 Jan 19. J Chem Theory Comput. 2016. PMID: 26744922 Free PMC article.
In the present work, the CHI-energy functions have been incorporated into the AutoDock Vina (ADV) scoring function, subsequently termed Vina-Carb (VC). Two user-adjustable parameters have been introduced, namely, a CHI- energy weight term (chi_coeff) that aff …
In the present work, the CHI-energy functions have been incorporated into the AutoDock Vina (ADV) scoring function, subsequent …
GlycoTorch Vina: Docking Designed and Tested for Glycosaminoglycans.
Boittier ED, Burns JM, Gandhi NS, Ferro V. Boittier ED, et al. J Chem Inf Model. 2020 Dec 28;60(12):6328-6343. doi: 10.1021/acs.jcim.0c00373. Epub 2020 Nov 5. J Chem Inf Model. 2020. PMID: 33152249
To overcome these challenges, we present GlycoTorch Vina (GTV), a molecular docking tool based on the carbohydrate docking program VinaCarb (VC). ...To aid in the rapid prototyping of future pose scoring functions, we include a module that allows users to include th …
To overcome these challenges, we present GlycoTorch Vina (GTV), a molecular docking tool based on the carbohydrate docking program Vi …
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685 results