Protein Hot Spots: The Islands of Stability

VMD: visual molecular dynamics

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Scalable molecular dynamics with NAMD

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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

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Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain

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Reaching for high-hanging fruit in drug discovery at protein–protein interfaces

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Proliferating cell nuclear antigen (PCNA): a dancer with many partners

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Structure of the C-Terminal Region of p21WAF1/CIP1 Complexed with Human PCNA

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Electrostatic aspects of protein–protein interactions

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Hot spots—A review of the protein–protein interface determinant amino‐acid residues

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Fundamental Aspects of Protein−Protein Association Kinetics

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Mapping of the p53 and mdm-2 Interaction Domains

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Convergent Solutions to Binding at a Protein-Protein Interface

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Strategies for Targeting Protein–Protein Interactions With Synthetic Agents

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Multiple diverse ligands binding at a single protein site: A matter of pre‐existing populations

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ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions

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A role for surface hydrophobicity in protein‐protein recognition

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Binding of small molecules to an adaptive protein–protein interface

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Predicting druggable binding sites at the protein–protein interface

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Crystal structure of the IL-2 signaling complex: Paradigm for a heterotrimeric cytokine receptor

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Discovery of a Potent Small Molecule IL-2 Inhibitor through Fragment Assembly

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Protein–Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking

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Transient Pockets on Protein Surfaces Involved in Protein−Protein Interaction

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Structural and Thermodynamic Analysis of Human PCNA with Peptides Derived from DNA Polymerase-δ p66 Subunit and Flap Endonuclease-1

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KFC Server: interactive forecasting of protein interaction hot spots

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Discovery and Optimization of Chromenotriazolopyrimidines as Potent Inhibitors of the Mouse Double Minute 2−Tumor Protein 53 Protein−Protein Interaction

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Structure of Free MDM2 N-terminal Domain Reveals Conformational Adjustments that Accompany p53-binding

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LOOPER: a molecular mechanics-based algorithm for protein loop prediction

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Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design

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Potent Small-Molecule Binding to a Dynamic Hot Spot on IL-2

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Closing the gaps among a web of DNA repair disorders

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Effects of Conformational Dynamics on Predicted Protein Druggability

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The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

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Modulators of Protein–Protein Interactions

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In silico structure-based approaches to discover protein-protein interaction-targeting drugs

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Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery

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DDMut-PPI: predicting effects of mutations on protein–protein interactions using graph-based deep learning

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Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design

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Superoxide Dismutase 1 (SOD1)-Derived Peptide Inhibits Amyloid Aggregation of Familial Amyotrophic Lateral Sclerosis SOD1 Mutants

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Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles

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An Overview of Computational Methods, Tools, Servers, and Databases for Drug Repurposing

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The Subtle Trade-Off between Evolutionary and Energetic Constraints in Protein–Protein Interactions

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Structure-Based Target Druggability Assessment

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A computational combinatorial approach identifies a protein inhibitor of superoxide dismutase 1 misfolding, aggregation, and cytotoxicity

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Using machine‐learning‐driven approaches to boost hot‐spot's knowledge

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Stabilization of bovine insulin against agitation-induced aggregation using RNA aptamers

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An α-helical peptidomimetic scaffold for dynamic combinatorial library formation

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HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid–protein interface with a case study

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Surface Dynamics in Allosteric Regulation of Protein-Protein Interactions: Modulation of Calmodulin Functions by Ca2+

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Homodimeric complexes of the 90–231 human prion: a multilayered computational study based on FMO/GRID-DRY approach

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In Silico Target Druggability Assessment: From Structural to Systemic Approaches

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Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and Amide 15N(1H) NMR Relaxation

Lesovoy, D., Roshchin, K., Sala, B. M., Sandalova, T., Achour, A., Agback, T., Agback, P., & Orekhov, V. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26188917 · Cited by 6 · see citing works

In silico engineering a CD80 variant with increased affinity to CTLA-4 and decreased affinity to CD28 for optimized cancer immunotherapy

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Molecular Dynamics Investigation on the Inhibition of MDM2‐p53 Interaction by Polyphenols

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Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD and Amide ¹⁵ N( ¹ H) NMR Relaxation

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Complementarity of stability patches at the interfaces of protein complexes: Implication for the structural organization of energetic hot spots

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In Silico Exploration of the Trypanothione Reductase (TryR) of L. mexicana

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Implication of Terminal Residues at Protein-Protein and Protein-DNA Interfaces

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Specific DNA sequences allosterically enhance protein–protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation

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Nanomechanics of PCNA: A protein-made DNA sliding clamp

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The role of protein “Stability patches” in molecular recognition: A case study of the human growth hormone‐receptor complex

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Protein-Protein Interactions (PPIs) as an Alternative to Targeting the ATP Binding Site of Kinase

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IFACE: A BIOINFORMATICS TOOL FOR THE ANALYSIS OF PROTEIN-PROTEIN INTERFACE

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Protein-Protein Interactions (PPIs) as an Alternative to Targeting the ATP Binding Site of Kinase

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Exploring the interaction hotspots of p-glycoprotein with herbal bioactives: In silico insights for integrative Ayurvedic therapeutics

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Complementarity of stability patches at the interfaces of protein complexes: Implication for the structural organization of energetic hot spots

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Hot Regions in Protein–Protein Interactions: The Organization and Contribution of Structurally Conserved Hot Spot Residues

Keskin, O., Ma, B., & Nussinov, R. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.10.077 · Cited by 519 · see citing works

Hot spots in protein–protein interfaces: Towards drug discovery

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Hot Spots at the Protein-Protein Interface

Kangueane, P., & Nilofer, C. (2018) · Springer eBooks · doi:10.1007/978-981-10-7347-2_7

Structural conservation of druggable hot spots in protein–protein interfaces

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