Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI

VMD: visual molecular dynamics

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A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations

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Anatomy of hot spots in protein interfaces

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Very fast prediction and rationalization of pKa values for protein–ligand complexes

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Langevin stabilization of molecular dynamics

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Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions

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

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

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Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects

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Energetics of protein-protein interactions: Analysis ofthe Barnase-Barstar interface by single mutations and double mutant cycles

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Identification of Vascular Endothelial Growth Factor Determinants for Binding KDR and FLT-1 Receptors

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Crystal Structure at 1.7 Å Resolution of VEGF in Complex with Domain 2 of the Flt-1 Receptor

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Bound water molecules and conformational stabilization help mediate an antigen-antibody association.

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Protein-protein recognition: Crystal structural analysis of a barnase-barstar complex at 2.0-.ANG. resolution

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

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Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering

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The bacterial cell‐division protein ZipA and its interaction with an FtsZ fragment revealed by X‐ray crystallography

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Computational alanine scanning mutagenesis—An improved methodological approach

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2006) · Journal of Computational Chemistry · doi:10.1002/jcc.20566 · Cited by 273 · see citing works

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy

Tunçbağ, N., Gürsoy, A., & Keskin, Ö. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp240 · Cited by 255 · see citing works

Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7

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An automated decision‐tree approach to predicting protein interaction hot spots

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APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility

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A feature-based approach to modeling protein–protein interaction hot spots

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Atomic Interactions and Profile of Small Molecules Disrupting Protein–Protein Interfaces: the TIMBAL Database

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KFC Server: interactive forecasting of protein interaction hot spots

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A Mutational Analysis of the Binding of Two Different Proteins to the Same Antibody

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The Contribution of Contact and Non-contact Residues of Antibody in the Affinity of Binding to Antigen

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Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction

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Unraveling the Importance of Protein−Protein Interaction: Application of a Computational Alanine-Scanning Mutagenesis to the Study of the IgG1 Streptococcal Protein G (C2 Fragment) Complex

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2006) · The Journal of Physical Chemistry B · doi:10.1021/jp054760d · Cited by 70 · see citing works

Unravelling Hot Spots: a comprehensive computational mutagenesis study

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2006) · Theoretical Chemistry Accounts · doi:10.1007/s00214-006-0151-z · Cited by 38 · see citing works

Hot Spot Occlusion from Bulk Water: a Comprehensive Study of the Complex between the Lysozyme HEL and the Antibody FVD1.3

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp067096p · Cited by 34 · see citing works

Accuracy of the numerical solution of the Poisson–Boltzmann equation

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2005) · Journal of Molecular Structure THEOCHEM · doi:10.1016/j.theochem.2004.12.049 · Cited by 30 · see citing works

Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective

Liu, Q., & Li, J. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-244 · Cited by 29 · see citing works

Protein–protein recognition: a computational mutagenesis study of the MDM2–P53 complex

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2008) · Theoretical Chemistry Accounts · doi:10.1007/s00214-008-0432-9 · Cited by 23 · see citing works

Detailed microscopic study of the full zipA:FtsZ interface

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20944 · Cited by 22 · see citing works

Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL‐10

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2006) · International Journal of Quantum Chemistry · doi:10.1002/qua.21193 · Cited by 22 · see citing works

ADAPT: A molecular mechanics approach for studying the structural properties of long DNA sequences

Lafontaine, I., & Lavery, R. (2000) · Biopolymers · doi:10.1002/1097-0282(2000)56:4 · Cited by 21 · see citing works

Empirical estimation of the energetic contribution of individual interface residues in structures of protein–protein complexes

Guharoy, M., & Chakrabarti, P. (2009) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-009-9282-3 · Cited by 20 · see citing works

CompASM: an Amber-VMD alanine scanning mutagenesis plug-in

Ribeiro, J. V., Cerqueira, N. M. F. S. A., Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2012) · Theoretical Chemistry Accounts · doi:10.1007/s00214-012-1271-2 · Cited by 16 · see citing works

Backbone Importance for Protein−Protein Binding

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007) · Journal of Chemical Theory and Computation · doi:10.1021/ct6003824 · Cited by 12 · see citing works

Detection of Farnesyltransferase Interface Hot Spots through Computational Alanine Scanning Mutagenesis

Perez, M. A. S., Sousa, S. F., Oliveira, E. F., Fernandes, P. A., & Ramos, M. J. (2011) · The Journal of Physical Chemistry B · doi:10.1021/jp205481y · Cited by 7 · see citing works

The chemistry of snake venom and its medicinal potential

de Oliveira, A. L. N., Viegas, M. F., Silva, S. L. D., Soares, A. M., Ramos, M. J., & Fernandes, P. A. (2022) · Nature Reviews Chemistry · doi:10.1038/s41570-022-00393-7 · Cited by 294 · see citing works

New insights into protein–protein interaction modulators in drug discovery and therapeutic advance

Nada, H., Choi, Y., Kim, S.-D., Jeong, K. S., Meanwell, N. A., & Lee, K. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-02036-3 · Cited by 233 · see citing works

Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions

Laraia, L., McKenzie, G. J., Spring, D. R., Venkitaraman, A. R., & Huggins, D. J. (2015) · Chemistry & Biology · doi:10.1016/j.chembiol.2015.04.019 · Cited by 152 · see citing works

Computational Alanine Scanning with Interaction Entropy for Protein–Ligand Binding Free Energies

Liu, X., Peng, L., Zhou, Y., Zhang, Y., & Zhang, J. Z. H. (2018) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b01295 · Cited by 120 · see citing works

Interaction Entropy for Computational Alanine Scanning

Yan, Y., Yang, M., Ji, C., & Zhang, J. Z. H. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00734 · Cited by 117 · see citing works

iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations

Geng, C., Vangone, A., Folkers, G. E., Xue, L. C., & Bonvin, A. M. J. J. (2019) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25630 · Cited by 82 · see citing works

Interaction entropy for computational alanine scanning in protein–protein binding

Qiu, L., Yan, Y., Sun, Z., Song, J., & Zhang, J. Z. H. (2017) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1342 · Cited by 63 · see citing works

Accurate and Efficient Calculation of Protein–Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants

Liu, X., Peng, L., & Zhang, J. Z. H. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00248 · Cited by 60 · see citing works

The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction

Li, Y., Cong, Y., Feng, G., Zhong, S., Zhang, J. Z. H., Sun, H., & Duan, L. (2018) · Structural Dynamics · doi:10.1063/1.5058172 · Cited by 56 · see citing works

Solvent Accessible Surface Area-Based Hot-Spot Detection Methods for Protein–Protein and Protein–Nucleic Acid Interfaces

Munteanu, C. R., Pimenta, A. C., Fernandez-Lozano, C., Melo, A., Cordeiro, M. N. D. S., & Moreira, I. S. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/ci500760m · Cited by 54 · see citing works

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces

Simões, I. C. M., Costa, I. P. D., Coimbra, J. T. S., Ramos, M. J., & Fernandes, P. A. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00378 · Cited by 52 · see citing works

Drug Repurposing Targeting Pseudomonas aeruginosa MvfR Using Docking, Virtual Screening, Molecular Dynamics, and Free-Energy Calculations

Vieira, T. F., Magalhães, R. P., Simões, M. V., & Sousa, S. F. (2022) · Antibiotics · doi:10.3390/antibiotics11020185 · Cited by 50 · see citing works

Solvent‐accessible surface area: How well can be applied to hot‐spot detection?

Martins, J. M. D. S., Ramos, R. M., Pimenta, A. C., & Moreira, I. S. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24413 · Cited by 48 · see citing works

Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of ParasiticSchistosoma mansoniCysteine Peptidase by Vinyl Sulfone Inhibitors

Fanfrlík, J., Brahmkshatriya, P. S., Řezáč, J., Jílková, A., Horn, M., Mares, M. A., Hobza, P., & Lepšı́k, M. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp409604n · Cited by 47 · see citing works

Molecular Docking and Molecular Dynamics (MD) Simulation of Human Anti-Complement Factor H (CFH) Antibody Ab42 and CFH Polypeptide

Yang, B. Y., Lin, S., Ren, J., Liu, T., Wang, Y., Li, C.-M., Xu, W., He, Y.-W., Zheng, W., Zhao, J. H., et al. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20102568 · Cited by 47 · see citing works

Computational Alanine Scanning Mutagenesis—An Improved Methodological Approach for Protein–DNA Complexes

Ramos, R. M., & Moreira, I. S. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400387r · Cited by 39 · see citing works

Simple Entropy Terms for End-Point Binding Free Energy Calculations

Menzer, W. M., Li, C., Sun, W.-D., Xie, B., & Minh, D. (2018) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.8b00418 · Cited by 36 · see citing works

Importance of IdoA and IdoA(2S) ring conformations in computational studies of glycosaminoglycan–protein interactions

Samsonov, S. A., & Pisabarro, M. T. (2013) · Carbohydrate Research · doi:10.1016/j.carres.2013.09.005 · Cited by 36 · see citing works

Computational analysis of hot spots and binding mechanism in the PD-1/PD-L1 interaction

Huang, D., Wen, W. X., Liu, X., Li, Y., & Zhang, J. Z. H. (2019) · RSC Advances · doi:10.1039/c9ra01369e · Cited by 32 · see citing works

A long-acting PAI-1 inhibitor reduces thrombus formation

Peng, S., Xue, G., Gong, L., Fang, C., Chen, J., Yuan, C., Chen, Z., Yao, L., Furie, B., & Huang, M. (2017) · Thrombosis and Haemostasis · doi:10.1160/th16-11-0891 · Cited by 28 · see citing works

Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA

Crean, R., Pudney, C. R., Cole, D. K., & van der Kamp, M. W. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00765 · Cited by 27 · see citing works

Calculation of hot spots for protein–protein interaction in p53/PMI‐MDM2/MDMX complexes

Huang, D., Qi, Y., Song, J., & Zhang, J. Z. H. (2018) · Journal of Computational Chemistry · doi:10.1002/jcc.25592 · Cited by 26 · see citing works

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2

Merski, M., Moreira, C., Abreu, R. M. V., Ramos, M. J., Fernandes, P. A., Martins, L. M., Pereira, P. J. B., & Macedo‐Ribeiro, S. (2017) · Cell Death and Disease · doi:10.1038/cddis.2017.487 · Cited by 24 · see citing works

Computational Simulation of HIV Protease Inhibitors to the Main Protease (Mpro) of SARS-CoV-2: Implications for COVID-19 Drugs Design

Yu, W., Wu, X., Zhao, Y., Chen, C., Yang, Z., Zhang, X., Ren, J., Wang, Y., Wu, C., Li, C., et al. (2021) · Molecules · doi:10.3390/molecules26237385 · Cited by 21 · see citing works

Insight Into the Binding Mechanism of p53/pDIQ-MDMX/MDM2 With the Interaction Entropy Method

Li, M., Cong, Y., Li, Y., Zhong, S., Wang, R., Li, H., & Duan, L. (2019) · Frontiers in Chemistry · doi:10.3389/fchem.2019.00033 · Cited by 20 · see citing works

Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax

Duan, L., Dong, S., Huang, K., Cong, Y., Luo, S., & Zhang, J. Z. H. (2021) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp04693k · Cited by 18 · see citing works

Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions

Delaunay, M., & Ha‐Duong, T. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1855-4_11 · Cited by 17 · see citing works

Structural and dynamic investigation of bovine folate receptor alpha (FOLR1), and role of ultra-high temperature processing on conformational and thermodynamic characteristics of FOLR1–folate complex

Sahoo, B. R., Maharana, J., Patra, M. C., Bhoi, G. K., Lenka, S. K., Dubey, P. K., Goyal, S., Dehury, B., & Pradhan, S. K. (2014) · Colloids and Surfaces B Biointerfaces · doi:10.1016/j.colsurfb.2014.05.028 · Cited by 17 · see citing works

Computational Investigation on the p53–MDM2 Interaction Using the Potential of Mean Force Study

Das, P., & Mattaparthi, V. S. K. (2020) · ACS Omega · doi:10.1021/acsomega.9b03372 · Cited by 16 · see citing works

Saturation Mutagenesis by Efficient Free-Energy Calculation

Jandová, Z., Fast, D., Setz, M., Pechlaner, M., & Oostenbrink, C. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b01099 · Cited by 16 · see citing works

A new scoring function for protein–protein docking that identifies native structures with unprecedented accuracy

Moreira, I. S., Martins, J. M. D. S., Coimbra, J. T. S., Ramos, M. J., & Fernandes, P. A. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp04688a · Cited by 15 · see citing works

Discovery of new druggable sites in the anti-cholesterol target HMG-CoA reductase by computational alanine scanning mutagenesis

Gesto, D., Cerqueira, N. M. F. S. A., Ramos, M. J., & Fernandes, P. A. (2014) · Journal of Molecular Modeling · doi:10.1007/s00894-014-2178-8 · Cited by 15 · see citing works

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

Rosário‐Ferreira, N., Bonvin, A. M. J. J., & Moreira, I. S. (2022) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1602 · Cited by 14 · see citing works

Binding Modes of Small‐Molecule Inhibitors to the EED Pocket of PRC2

Huang, D., Tian, S., Qi, Y., & Zhang, J. Z. H. (2019) · ChemPhysChem · doi:10.1002/cphc.201900903 · Cited by 14 · see citing works

Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarization

Tian, S., Ji, C., & Zhang, J. Z. H. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1713892 · Cited by 14 · see citing works

Functional inhibition of c-Myc using novel inhibitors identified through “hot spot” targeting

Singh, A. K., Kumar, P., Sarvagalla, S., Bharadwaj, T., Nayak, N., Coumar, M. S., Giri, R., & Garg, N. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101898 · Cited by 14 · see citing works

Glutamine Synthetase Drugability beyond Its Active Site: Exploring Oligomerization Interfaces and Pockets

Moreira, C., Ramos, M. J., & Fernandes, P. A. (2016) · Molecules · doi:10.3390/molecules21081028 · Cited by 12 · see citing works

Computer aided design and NMR characterization of an oligopeptide targeting the Ebola virus VP24 protein

Dapiaggi, F., Pieraccini, S., Potenza, D., Vasile, F., Macut, H., Pellegrino, S., Aliverti, A., & Sironi, M. (2017) · New Journal of Chemistry · doi:10.1039/c6nj04014d · Cited by 11 · see citing works

Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor

Cong, Y., Duan, L., Huang, K., Bao, J., & Zhang, J. Z. H. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1734488 · Cited by 10 · see citing works

Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition

Silva, P. J., & Bernardo, C. E. P. (2014) · PeerJ · doi:10.7717/peerj.470 · Cited by 10 · see citing works

Water Bridges Play a Key Role in Affinity and Selectivity for Malarial Protease Falcipain-2

González, J. E. H., Alvarez, L. H., Leite, V. B. P., & Pascutti, P. G. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00294 · Cited by 10 · see citing works

Modern Strategies for the Diversification of the Supply of Natural Compounds: The Case of Alkaloid Painkillers

Sousa, J. P. M., Ramos, M. J., & Fernandes, P. A. (2021) · ChemBioChem · doi:10.1002/cbic.202100623 · Cited by 9 · see citing works

Binding free energy calculations on E‐selectin complexes with sL ex oligosaccharide analogs

Barra, P. A., Ribeiro, A. J. M., Ramos, M. J., Jiménez, V. A., Alderete, J. B., & Fernandes, P. A. (2016) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12837 · Cited by 8 · see citing works

Characterizing the hotspots involved in RON-MSPβ complex formation using in silico alanine scanning mutagenesis and molecular dynamics simulation

Zarei, O., Hamzeh‐Mivehroud, M., Benvenuti, S., Alkan, F. Ü., & Dastmalchi, S. (2017) · Advanced Pharmaceutical Bulletin · doi:10.15171/apb.2017.018 · Cited by 8 · see citing works

An efficient method to predict protein thermostability in alanine mutation

Gao, Y., Wang, B., Hu, S., Zhu, T., & Zhang, J. Z. H. (2022) · Physical Chemistry Chemical Physics · doi:10.1039/d2cp04236c · Cited by 7 · see citing works

Molecular determinants of tetramerization in the KcsA cytoplasmic domain

Kamnesky, G., Hirschhorn, O., Shaked, H., Chen, J., Yao, L., & Chill, J. H. (2014) · Protein Science · doi:10.1002/pro.2525 · Cited by 7 · see citing works

Molecular insight into multiple RpoB clinical mutants of Mycobacterium tuberculosis: An attempt to probe structural variations in rifampicin binding site underlying drug resistance

Srivastava, G., Tripathi, S., Kumar, A., & Sharma, A. K. (2018) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2018.06.184 · Cited by 7 · see citing works

Properties that rank protein:protein docking poses with high accuracy

Simões, I. C. M., Coimbra, J. T. S., Neves, R. P. P., Costa, I. P. D., Ramos, M. J., & Fernandes, P. A. (2018) · Physical Chemistry Chemical Physics · doi:10.1039/c8cp03888k · Cited by 7 · see citing works

Design and synthesis of BRC analogous peptides and their interactions with a key p53 peptide

Zhao, D., Lü, K., Liu, G., Ma, L., Zhu, H., & He, J. (2018) · FEBS Letters · doi:10.1002/1873-3468.13256 · Cited by 7 · see citing works

Alchemical Calculation of Relative Free Energies for Charge-Changing Mutations at Protein–Protein Interfaces Considering Fixed and Variable Protonation States

González, J. E. H., & de Araújo, A. S. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00972 · Cited by 6 · see citing works

Discovery of New Sites for Drug Binding to the Hypertension‐Related Renin–Angiotensinogen Complex

Brás, N. F., Fernandes, P. A., & Ramos, M. J. (2013) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12258 · Cited by 6 · see citing works

Exploring the Desumoylation Process of SENP1: A Study Combined MD Simulations with QM/MM Calculations on SENP1-SUMO1-RanGAP1

Shi, T., Han, Y., Li, W., Zhao, Y., Liu, Y., Huang, Z., Lu, S., & Zhang, J. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci4002487 · Cited by 6 · see citing works

Structure-based discovery of novel small molecule inhibitors of platelet-derived growth factor-B

Zarei, O., Sarri, N., Dastmalchi, S., Zokai, F., Papadopoulos, N., Lennartsson, J., Heldin, C., & Hamzeh‐Mivehroud, M. (2019) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2019.103374 · Cited by 6 · see citing works

Ligand Reorganization for End-Point Binding Free Energy Calculations: Identifying Preferred Poses of Fentanyls in the μ Opioid Receptor

Minh, D. D. L., Cooper, D. A., Xie, B., & Shi, L. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01073 · Cited by 5 · see citing works

Conformational states of HAMP domains interacting with sensory rhodopsin membrane systems: an integrated all-atom and coarse-grained molecular dynamics simulation approach

Sahoo, B. R., & Fujiwara, T. (2016) · Molecular BioSystems · doi:10.1039/c6mb00730a · Cited by 5 · see citing works

The interaction of InvF-RNAP is mediated by the chaperone SicA in Salmonella sp: an in silico prediction

Farias, A. B., Cortés-Avalos, D., Ibarra, J. A., & Pérez‐Rueda, E. (2024) · PeerJ · doi:10.7717/peerj.17069 · Cited by 4 · see citing works

Relational dynamics obtained through simulation studies of thioredoxin reductase: From a multi-drug resistant Entamoeba histolytica

Shahzadi, Z., Abbas, G., & Azam, S. S. (2020) · Journal of Molecular Liquids · doi:10.1016/j.molliq.2020.112939 · Cited by 4 · see citing works

Protein–Protein Interactions as Promising Molecular Targets for Novel Antimicrobials Aimed at Gram-Negative Bacteria

Maj, P., & Trylska, J. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms262210861 · Cited by 4 · see citing works

Calculation of PARP1-ligand binding free energy using alanine scanning and interaction entropy method

Zhang, Y., Liu, X., Zhou, Y., & Zhang, J. Z. H. (2017) · Scientia Sinica Chimica · doi:10.1360/n032017-00161 · Cited by 3 · see citing works

Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations

Kasavajhala, K., & Simmerling, C. L. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00005 · Cited by 3 · see citing works

Design, synthesis and interaction of BRC4 analogous peptides with RAD51(241–260)

Li, J., Lü, K., Lv, M., Liu, G., Ma, L., & Qi, J. (2019) · Amino Acids · doi:10.1007/s00726-019-02813-3 · Cited by 3 · see citing works

Binding Mechanism of Thrombin–Ligand Systems Investigated by a Polarized Protein-Specific Charge Force Field and Interaction Entropy Method

Zhong, S., Huang, K., Xiao, Z., Sheng, X., Li, Y., & Duan, L. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.9b08064 · Cited by 3 · see citing works

Computational Biochemistry

Brás, N. F., Coimbra, J. T. S., Neves, R. P. P., Cerqueira, N. M. F. S. A., Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-409547-2.10833-9 · Cited by 2 · see citing works

Protein-Peptide Interactions in Regulatory Events

Raghavender, U. S., & Rathore, R. S. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.90694-0 · Cited by 2 · see citing works

Epitopes mapped onto SARS-CoV-2 receptor-binding motif by five distinct human neutralising antibodies

Gutiérrez, L. J., Tosso, R. D., Zarycz, M. N. C., Enriz, R., & Baldoni, H. (2022) · Molecular Simulation · doi:10.1080/08927022.2022.2111421 · Cited by 1 · see citing works

A Charge-Reversal Point Mutation Completely Depletes Flavin Chromophore from European Robin Cryptochrome 4a Protein

Xu, J., Sjulstok, E., Berthias, F., Schmidt, J., Mouritsen, H., Jensen, O. N., & Solov’yov, I. A. (2026) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.5c03833 · Cited by 1 · see citing works

Gene hunting and semi-rational design of carbonyl reductase from Kosakonia radicincitans for highly efficient synthesis of the key chiral intermediate of Telotristat ethyl

Zhang, H., Ning, P., Liu, H., Qian, F., Wang, Y., & Wang, P. (2024) · Molecular Catalysis · doi:10.1016/j.mcat.2024.114573 · Cited by 1 · see citing works

Design of BRC analogous peptides based on the complex BRC8–RAD51 and the preliminary study on the peptide structures

Zhao, D., Lü, K., Liu, G., Zhu, H., Ma, L., Qi, J., & Yuan, L. (2020) · Amino Acids · doi:10.1007/s00726-020-02856-x

Computational Investigation on the MDM2-Idasanutlin Interaction Using the Potential of Mean Force Method

Das, P., & Mattaparthi, V. S. K. (2021) · Current Chemical Biology · doi:10.2174/2212796815666210716151211

Peer Review #1 of "Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition (v0.1)"

(2014) · PeerJ · doi:10.7287/peerj.470v0.1/reviews/1

Peer Review #2 of "Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition (v0.1)"

(2014) · PeerJ · doi:10.7287/peerj.470v0.1/reviews/2

Computational alanine scanning with GBSA and interaction entropy: a review of methodologies and applications in protein–protein and protein–ligand binding

Liu, X., Xu, X., Duan, L. L., & Zhang, J. Z. H. (2026) · Chemical Science · doi:10.1039/d6sc04176k

Computational alanine scanning mutagenesis—An improved methodological approach

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2006) · Journal of Computational Chemistry · doi:10.1002/jcc.20566 · Cited by 273 · see citing works

Unravelling Hot Spots: a comprehensive computational mutagenesis study

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2006) · Theoretical Chemistry Accounts · doi:10.1007/s00214-006-0151-z · Cited by 38 · see citing works

CompASM: an Amber-VMD alanine scanning mutagenesis plug-in

Ribeiro, J. V., Cerqueira, N. M. F. S. A., Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2012) · Highlights in theoretical chemistry · doi:10.1007/978-3-642-41163-2_8 · Cited by 1 · see citing works

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces

Simões, I. C. M., Costa, I. P. D., Coimbra, J. T. S., Ramos, M. J., & Fernandes, P. A. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00378 · Cited by 52 · see citing works

Unraveling the Importance of Protein−Protein Interaction: Application of a Computational Alanine-Scanning Mutagenesis to the Study of the IgG1 Streptococcal Protein G (C2 Fragment) Complex

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2006) · The Journal of Physical Chemistry B · doi:10.1021/jp054760d · Cited by 70 · see citing works