Hierarchy of Regions of Amino Acid Sequence with Respect to Their Role in the Protein Spatial Structure. - Igor N. Berezovsky; Natalia G. Esipova; Vladimir G. Tumanyan (J. Comput. Biol., 2000)

Entropic Stabilization of Proteins and Its Proteomic Consequences. - Igor N. Berezovsky; William W. Chen; Paul J. Choi; Eugene I. Shakhnovich (PLoS Comput. Biol., 2005)

Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. - Georg Schneider 001; Georg Neuberger; Michael Wildpaner; Sun Tian; Igor N. Berezovsky; Frank Eisenhaber (BMC Bioinform., 2006)

Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins. - Igor N. Berezovsky; Konstantin B. Zeldovich; Eugene I. Shakhnovich (PLoS Comput. Biol., 2007)

Protein and DNA Sequence Determinants of Thermophilic Adaptation. - Konstantin B. Zeldovich; Igor N. Berezovsky; Eugene I. Shakhnovich (PLoS Comput. Biol., 2007)

Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure. - Grzegorz Koczyk; Igor N. Berezovsky (Nucleic Acids Res., 2008)

Prototypes of elementary functional loops unravel evolutionary connections between protein functions. - Alexander Goncearenco; Igor N. Berezovsky (Bioinform., 2010)

Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins. - Alexander Goncearenco; Igor N. Berezovsky (Bioinform., 2011)

Binding Leverage as a Molecular Basis for Allosteric Regulation. - Simon Mitternacht; Igor N. Berezovsky (PLoS Comput. Biol., 2011)

Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication. - Simon Mitternacht; Igor N. Berezovsky (PLoS Comput. Biol., 2011)

SPACER: server for predicting allosteric communication and effects of regulation. - Alexander Goncearenco; Simon Mitternacht; Taipang Yong; Birgit Eisenhaber; Frank Eisenhaber; Igor N. Berezovsky (Nucleic Acids Res., 2013)

Nucleotide binding database NBDB - a collection of sequence motifs with specific protein-ligand interactions. - Zejun Zheng; Alexander Goncearenco; Igor N. Berezovsky (Nucleic Acids Res., 2016)

Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication. - Enrico Guarnera; Igor N. Berezovsky (PLoS Comput. Biol., 2016)

AlloSigMA: allosteric signaling and mutation analysis server. - Enrico Guarnera; Zhen Wah Tan; Zejun Zheng; Igor N. Berezovsky (Bioinform., 2017)

Exploring chromatin hierarchical organization via Markov State Modelling. - Zhen Wah Tan; Enrico Guarnera; Igor N. Berezovsky (PLoS Comput. Biol., 2018)

Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response. - Wei-Ven Tee; Enrico Guarnera; Igor N. Berezovsky (PLoS Comput. Biol., 2018)

AlloMAPS: allosteric mutation analysis and polymorphism of signaling database. - Zhen Wah Tan; Wei-Ven Tee; Enrico Guarnera; Lauren Booth; Igor N. Berezovsky (Nucleic Acids Res., 2019)

AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations. - Zhen Wah Tan; Enrico Guarnera; Wei-Ven Tee; Igor N. Berezovsky (Nucleic Acids Res., 2020)

Deriving and Using Descriptors of Elementary Functions in Rational Protein Design. - Melvin Yin; Alexander Goncearenco; Igor N. Berezovsky (Frontiers Bioinform., 2021)

AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design. - Zhen Wah Tan; Wei-Ven Tee; Enrico Guarnera; Igor N. Berezovsky (Nucleic Acids Res., 2023)