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Protein structure networks

An Integrative Computational Framework Based on a Two-Step Random Forest Algorithm Improves Prediction of Zinc-Binding Sites in Proteins

Cheng Zheng, Mingjun Wang, [ ... ], Jiangning Song

FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model

Mingjun Wang, Xing-Ming Zhao, [ ... ], Jiangning Song

Morphology and Viscoelasticity of Actin Networks Formed with the Mutually Interacting Crosslinkers: Palladin and Alpha-actinin

Brian Grooman, Ikuko Fujiwara, Carol Otey, Arpita Upadhyaya

Mapping the Mutual Information Network of Enzymatic Families in the Protein Structure to Unveil Functional Features

Daniel Aguilar, Baldo Oliva, Cristina Marino Buslje

Identification of Catalytic Residues Using a Novel Feature that Integrates the Microenvironment and Geometrical Location Properties of Residues

Lei Han, Yong-Jun Zhang, [ ... ], Ziding Zhang

Hemoglobin Interactions with αB Crystallin: A Direct Test of Sensitivity to Protein Instability

Tyler J. W. Clark, Scott A. Houck, John I. Clark

Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

Elena Papaleo, Giulia Renzetti, Matteo Tiberti

Why Do Protein Folding Rates Correlate with Metrics of Native Topology?

Patrícia F. N. Faísca, Rui D. M. Travasso, Andrea Parisi, Antonio Rey

Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks

Frank Emmert-Streib

Markov Dynamics as a Zooming Lens for Multiscale Community Detection: Non Clique-Like Communities and the Field-of-View Limit

Michael T. Schaub, Jean-Charles Delvenne, Sophia N. Yaliraki, Mauricio Barahona

Calculating Ensemble Averaged Descriptions of Protein Rigidity without Sampling

Luis C. González, Hui Wang, Dennis R. Livesay, Donald J. Jacobs

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

Rohita Sinha, Petras J. Kundrotas, Ilya A. Vakser

Modularity in Protein Complex and Drug Interactions Reveals New Polypharmacological Properties

Jose C. Nacher, Jean-Marc Schwartz

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