Protein Evolution

Distant Homology BLASTP Searches identify Neuropeptide Counterparts across Species.- Predicting Protein Folding Dynamics using Sequence Information.- Predictive Model for Single-site Mutations that change Intrinsically Disordered Protein Binding Energetics.- Detection of Specificity-determining Positions in Protein Families.- Co-Var, a measure to determine intra-protein, inter-protein, protein-DNA or protein-RNA co-evolution.- adabmDCA 2.0 - A flexible but easy-to-use package for direct coupling analysis.- Unlocking Protein Evolution Insights: Efficient and Interpretable Mutational Effect Predictions with GEMME.- Using Total Network Dissimilarity to Analyze Protein Structures across Homologs.- Allosteric Network Analysis Toolkit for Single-Domain PhosphoProteins.- Computational identification of potential shape-shifting proteins from structures.- Transition state-based computational enzyme design.- Quantification of conformational changes of kinase regulators, kinases and regulator - kinase complexes using the TSR algorithm.- Identifying functional Water Encapsulation Sites within the Transmembrane Domain of Sensor Kinases.- Protein-Protein Interaction Site Prediction via EquiPPIS and its Application in Studying Viral Replication.- Modeling protein-protein complexes by combining pyDock and AlphaFold.- Binding affinity prediction of membrane protein-protein complexes using MPA-Pred.- Computational Methods to Engineer Cas Proteins for Efficient Genome Editing.- Exploring the Functional Consequences of Protein-Coding Alternative Splice Variants at a Genome scale: A Guide to Utilizing Expansion.