Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies

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

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Wild-type p53 activates transcription in vitro

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Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

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MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

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Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding

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A simple physical model for binding energy hot spots in protein–protein complexes

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Molecular Recognition and Docking Algorithms

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Unraveling hot spots in binding interfaces: progress and challenges

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Inhibiting the p53–MDM2 interaction: an important target for cancer therapy

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Combining docking and molecular dynamic simulations in drug design

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Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA

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Computer-aided drug design platform using PyMOL

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Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces

Ma, B., Elkayam, T., Wolfson, H., & Nussinov, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1030237100 · Cited by 595

Computational Alanine Scanning of Protein-Protein Interfaces

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Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX

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BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

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Helical β-Peptide Inhibitors of the p53-hDM2 Interaction

Kritzer, J. A., Lear, J. D., Hodsdon, M. E., & Schepartz, A. (2004) · Journal of the American Chemical Society · doi:10.1021/ja031625a · Cited by 314

Computational alanine scanning of the 1:1 human growth hormone–receptor complex

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Computational redesign of protein-protein interaction specificity

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Conservation of polar residues as hot spots at protein interfaces

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Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications

Limo, M. J., Sola-Rabada, A., Boix, E., Thota, V., Westcott, Z. C., Puddu, V., & Perry, C. C. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00660 · Cited by 287

Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes

Beard, H., Cholleti, A., Pearlman, D., Sherman, W., & Loving, K. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0082849 · Cited by 273

Computational alanine scanning mutagenesis—An improved methodological approach

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007) · Journal of Computational Chemistry · doi:10.1002/jcc.20566 · Cited by 273

Systematic Targeting of Protein–Protein Interactions

Modell, A. E., Blosser, S. L., & Arora, P. S. (2016) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2016.05.008 · Cited by 184

Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex

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Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity

Li, M., Petukh, M., Alexov, E., & Panchenko, A. R. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct401022c · Cited by 111

Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods

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Fragment Informatics and Computational Fragment‐Based Drug Design: An Overview and Update

Sheng, C., & Zhang, W. (2013) · Medicinal Research Reviews · doi:10.1002/med.21255 · Cited by 80

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI

Martins, S. A., Perez, M. A. S., Moreira, I. S., Sousa, S. F., Ramos, M. J., & Fernandes, P. A. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct4000372 · Cited by 72

A multiscale approach to predicting affinity changes in protein-protein interfaces: Multiscale Method for Predicting ΔΔG

Dourado, D. F. A. R., & Flores, S. C. (2014) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.24634 · Cited by 56

Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis

Cong, Y., Feng, Y., Ni, H., Zhi, F., Miao, Y., Fang, B., Zhang, L., & Zhang, J. Z. H. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00241 · Cited by 40

Decoding selectivity: computational insights into AKR1B1 and AKR1B10 inhibition

Liu, M., Qin, X., Li, J., Jiang, Y., Jiang, J., Guo, J., Xu, H., Wang, Y., Bi, H., & Wang, Z. (2024) · Physical Chemistry Chemical Physics · doi:10.1039/d3cp05985e · Cited by 7