Our algorithms process large data sets within a minute. by Manu Aggarwal (15990691)

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

“…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)

“…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. …”

Genetic algorithms can be applied to higher-dimensional design problems. by Lu Hong (399882)

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Algorithmic assessment reveals functional implications of GABRD gene variants linked to idiopathic generalized epilepsy by Ayla Arslan (17943365)

“…Initially, separate algorithms based on sequence homology are utilized to assess this variant set. …”

NRPStransformer, an Accurate Adenylation Domain Specificity Prediction Algorithm for Genome Mining of Nonribosomal Peptides by Zhihan Zhang (1403308)

“…Leveraging the sequences within the flavodoxin-like subdomain, we developed a substrate specificity prediction algorithm using a protein language model, achieving 92% overall prediction accuracy for 43 frequently observed amino acids, significantly improving the prediction reliability. …”

Super.Complex identifies likely protein complexes within a PPI network using a distributed supervised AutoML method. by Meghana Venkata Palukuri (11890672)

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

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Identification of hub genes from the PPI network by bottleneck algorithm using the cytoHubba Cytoscape plugin. by Cihat Erdogan (12529243)

Core genes were selected through PPI analysis based on three algorithms. by Dong-Hee Han (140305)

“…<p>Among 46 DEGs whose expression significantly changed in A549 and BEAS-2B cell lines, the core genes were selected using three algorithms: MCC, MNC, and DEGREE. <b>(A)</b> The top 10 genes were prioritized using MCC analysis, which identifies the largest clique within the PPI network and selects the central proteins within the clique. …”

Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking by Hahnbeom Park (665004)

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Automated correction of fluorescence bleedthrough in the larval eye. by Sebastian M. Bernasek (8525829)

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Fly-QMA: Automated analysis of mosaic imaginal discs in <i>Drosophila</i> by Sebastian M. Bernasek (8525829)

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Conventional versus quantitative mosaic analysis. by Sebastian M. Bernasek (8525829)

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Protein-Protein Interaction (PPI) and ceRNA Regulatory Network Analysis. by Jie Chu (293795)

Morpheus: A fragment-based algorithm to predict metamorphic behaviour in proteins across proteomes by Vijay Subramanian (20718933)

“…<p dir="ltr">Supplementary material for Morpheus: A fragment-based algorithm to predict metamorphic behaviour in proteins across proteomes.…”

Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta by Morgan L. Nance (10981871)

“…In this work, we introduce <i>GlycanDock</i>, a residue-centric protein–glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. …”

Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta by Morgan L. Nance (10981871)

“…In this work, we introduce <i>GlycanDock</i>, a residue-centric protein–glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. …”

Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta by Morgan L. Nance (10981871)

“…In this work, we introduce <i>GlycanDock</i>, a residue-centric protein–glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. …”

Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta by Morgan L. Nance (10981871)

“…In this work, we introduce <i>GlycanDock</i>, a residue-centric protein–glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. …”