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

Subjects:

3D modeling qualities of the AS single-template models built by including DOPE in the objective function of MODELLER. by Giacomo Janson (8138517)

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

“…<div><p>Genome-scale metabolic models (GEMs) are mathematically structured knowledge bases of metabolism that provide phenotypic predictions from genomic information. 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. …”

Pairwise alignment results from human proteins and <i>H</i>. <i>pylori</i> proteins using Blosum 62 and PM250 algorithms. by Andrés Sánchez Caraballo (15354081)

3D modeling qualities of the AM multiple-template models built by including DOPE in the objective function of MODELLER. by Giacomo Janson (8138517)

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

Depiction of the theory, can sequence infer function? by Ashley I. Heinson (8124374)

Rosetta energy functions for membrane proteins cannot identify the inward-facing conformation of PfMATE. by Diego del Alamo (9925083)

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. …”

A comparative workflow of all six functional software tools producing GO term lists from the same dataset. by Ray Sajulga (5721518)

Cost functions implemented in Neuroptimus. by Máté Mohácsi (20469514)

Dynamical comparison between Drosha and Dicer reveals functional motion similarities and dissimilarities by Rotem Aharoni (8108177)

“…Since dynamics is essential for protein function, a comparison at their dynamics level is fundamental for a complete understanding of the overall relations between these proteins. …”

Description: Subnetwork of TFRC from functional tissue network of PDAC. by Enze Liu (6286262)

PATH has state-of-the-art performance versus previous binding affinity prediction algorithms. by Yuxi Long (11024307)

Subjects:

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

Description: Subnetwork of TFRC from functional cell-line network of PDAC. by Enze Liu (6286262)

MEDOC: A Fast, Scalable, and Mathematically Exact Algorithm for the Site-Specific Prediction of the Protonation Degree in Large Disordered Proteins by Martin J. Fossat (3714079)

Subjects: “…mathematically exact algorithm…”

Fraction of selective neurons as a function of the imaging signal-to-noise ratio. by Ziqiang Wei (5953964)

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

Subjects:

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. …”