Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy by Yujin Wu (2901128)

“…However, only a few attempts to include the side chain conformational entropy upon binding within the application of flexible receptor docking methodology exist. Here, we propose a new physics-based scoring function that includes both enthalpic and entropic contributions upon binding by considering the conformational variability of the flexible side chains within the ensemble of docked poses. …”

Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy by Yujin Wu (2901128)

“…However, only a few attempts to include the side chain conformational entropy upon binding within the application of flexible receptor docking methodology exist. Here, we propose a new physics-based scoring function that includes both enthalpic and entropic contributions upon binding by considering the conformational variability of the flexible side chains within the ensemble of docked poses. …”

BOFdat Step 3: Identifying species-specific metabolic end goals. by Jean-Christophe Lachance (6619307)

“…(C) Schematic representation of the implementation of the genetic algorithm (GA) using the metabolic network presented in B. …”

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses by Dominykas Lukauskis (14143149)

“…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …”

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses by Dominykas Lukauskis (14143149)

“…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …”

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses by Dominykas Lukauskis (14143149)

“…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …”

Greedy optimization algorithm. by Alexis Bénichou (19832361)

Code snippets to add user-specific custom functionality in PyNoetic. by Gursimran Singh (575288)

Subjects:

Python implementation from Symplectic decomposition from submatrix determinants by Jason L. Pereira (11598632)

“…Python implementation of the algorithm and demonstration of how to use the functions.…”

Illustration of the unrestricted model and its training algorithm. by Yuru Song (21300760)

GraSPy: an Open Source Python Package for Statistical Connectomics by Benjamin Pedigo (6580352)

“…We developed GraSPy, an open-source Python toolkit for statistical inference on graphs. …”

Modular architecture design of PyNoetic showing all its constituent functions. by Gursimran Singh (575288)

Subjects:

Adaptive H-REMD simulation algorithm. by Danial Pourjafar-Dehkordi (7165523)

The workflow used to analyze imbalanced and balanced sequences. by Solomon Shiferaw Beyene (9143178)

Performances of Naïve Bayes (NB), Multilayer Perceptron (MLP), Random Forest (RF), Gradient Boosting (GB), Support Vector Machine (SVM) and K- Nearest Neighbors (KNN). by Solomon Shiferaw Beyene (9143178)

Accuracy, sensitivity, specificity and F-score. by Solomon Shiferaw Beyene (9143178)

The figures showed a comparison of the balanced and imbalanced sequences and performance of classifiers. by Solomon Shiferaw Beyene (9143178)

Comparison of PyNoetic’s functionality for BCI design with other existing state-of-the-art frameworks. by Gursimran Singh (575288)

Subjects:

Step by step comparison of enrichment algorithms. by Nicholas Markarian (18251668)

Pictorial representation of the edge-cutting algorithm. by Pratik Mullick (12851011)