A Functional Bayesian Model for Hydrogen–Deuterium Exchange Mass Spectrometry by Oliver M. Crook (6013703)

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Mutations at functionally important interfaces. by Myo T. Naung (10873278)

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PATH (with persistence fingerprint) runs significantly faster than TNet-BP, a representative binding affinity prediction algorithm that uses persistent homology, on larger protein-... by Yuxi Long (11024307)

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Fig 7 - by Paolo Perlasca (9909695)

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Hierarchical communities obtained from CoV-human network using the “community-based” visualization option provided by UNIPred-Web. by Paolo Perlasca (9909695)

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Internal symmetry in crystallin proteins. by Spencer E. Bliven (6672755)

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ADT: A Generalized Algorithm and Program for Beyond Born–Oppenheimer Equations of “<i>N</i>” Dimensional Sub-Hilbert Space by Koushik Naskar (7510592)

“…In order to overcome such shortcoming, we develop a generalized algorithm, “ADT” to generate the nonadiabatic equations through symbolic manipulation and to construct highly accurate diabatic surfaces for molecular processes involving excited electronic states. …”

NLDock: a Fast Nucleic Acid–Ligand Docking Algorithm for Modeling RNA/DNA–Ligand Complexes by Yuyu Feng (11371729)

“…Here, we have developed a fast nucleic acid–ligand docking algorithm, named NLDock, by implementing our intrinsic scoring function ITScoreNL for nucleic acid–ligand interactions into a modified version of the MDock program. …”

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. …”

Supplementary Files 1-11 from Protein Signatures of NK Cell–Mediated Melanoma Killing Predict Response to Immunotherapies by Sabrina Cappello (14950324)

Ramachandran plot of wild and mutant GRIN2A protein derived from PROCHECK. by Ishtiaque Ahammad (10522854)

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BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data by Jean-Christophe Lachance (6619307)

“…GEM-guided predictions of growth phenotypes rely on the accurate definition of a biomass objective function (BOF) that is designed to include key cellular biomass components such as the major macromolecules (DNA, RNA, proteins), lipids, coenzymes, inorganic ions and species-specific components. …”

Examples of protein globular domains with internal symmetry. by Spencer E. Bliven (6672755)

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Molecular Graph-Based Deep Learning Algorithm Facilitates an Imaging-Based Strategy for Rapid Discovery of Small Molecules Modulating Biomolecular Condensates by Peng Gao (35465)

“…Furthermore, we validated that these candidates do not affect the normal splicing function of TDP-43. Taken together, a combination of an imaging-based screen and a GCN-based deep learning method dramatically improves the speed and accuracy of the compound screen for biomolecular condensates.…”

Molecular Graph-Based Deep Learning Algorithm Facilitates an Imaging-Based Strategy for Rapid Discovery of Small Molecules Modulating Biomolecular Condensates by Peng Gao (35465)

“…Furthermore, we validated that these candidates do not affect the normal splicing function of TDP-43. Taken together, a combination of an imaging-based screen and a GCN-based deep learning method dramatically improves the speed and accuracy of the compound screen for biomolecular condensates.…”

Pseudocode of the RPath algorithm. by Daniel Domingo-Fernández (5432273)

“…<p>Given a KG, drug, disease and a defined path length (i.e., <i>lmax)</i>, the core function of the algorithm, <i>is_drug_prioritized</i>, returns whether a drug should be prioritized or not. …”

Differences between average F1 obtained for PFP-WGAN and DeepGO-Seq for the GO terms in each height ( and ). by Seyyede Fatemeh Seyyedsalehi (10196767)

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Table_4_A Comparative Study of Cluster Detection Algorithms in Protein–Protein Interaction for Drug Target Discovery and Drug Repurposing.xlsx by Jun Ma (9393)

“…However, the functions inferred for these topological modules extracted from a large-scale molecular interaction network, such as a protein–protein interaction (PPI) network, could differ depending on different cluster detection algorithms. …”