Free-energy landscape of protein oligomerization from atomistic simulations

Comparison of simple potential functions for simulating liquid water

Jorgensen, W. L., Chandrasekhar, J., Madura, J., Impey, R., & Klein, M. (1983) · The Journal of Chemical Physics · doi:10.1063/1.445869 · Cited by 38,335 · see citing works

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. R. (2008) · Journal of Chemical Theory and Computation · doi:10.1021/ct700301q · Cited by 15,830 · see citing works

Improved side-chain torsion potentials for the Amber ff99SB protein force field

Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J., Dror, R., & Shaw, D. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22711 · Cited by 6,037 · see citing works

Escaping free-energy minima

Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626 · see citing works

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

Barducci, A., Bussi, G., & Parrinello, M. (2008) · Physical Review Letters · doi:10.1103/physrevlett.100.020603 · Cited by 3,184 · see citing works

Atomic-level characterization of the structural dynamics of proteins

Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., Bank, J. A., Jumper, J. M., Salmon, J. K., Shan, Y., et al. (2010) · Science · doi:10.1126/science.1187409 · Cited by 1,923 · see citing works

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., Donadio, D., Marinelli, F., Pietrucci, F., Broglia, R. A., et al. (2009) · Computer Physics Communications · doi:10.1016/j.cpc.2009.05.011 · Cited by 1,890 · see citing works

Metadynamics

Barducci, A., Bonomi, M., & Parrinello, M. (2011) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.31 · Cited by 1,217 · see citing works

Parallel tempering algorithm for conformational studies of biological molecules

Hansmann, U. H. E. (1997) · Chemical Physics Letters · doi:10.1016/s0009-2614(97)01198-6 · Cited by 1,003 · see citing works

Speeding molecular recognition by using the folding funnel: The fly-casting mechanism

Shoemaker, B. A., Portman, J. J., & Wolynes, P. G. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.160259697 · Cited by 971 · see citing works

Parallel Tempering Algorithm for Conformational Studies of Biological MoleculesPreprint

Hansmann, U. H. E. (1997) · Cited by 886 · see citing works

Fundamental Aspects of Protein−Protein Association Kinetics

Schreiber, G., Haran, G., & Zhou, H. (2009) · Chemical Reviews · doi:10.1021/cr800373w · Cited by 739 · see citing works

The power of two: protein dimerization in biology

Marianayagam, N. J., Sunde, M., & Matthews, J. M. (2004) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2004.09.006 · Cited by 596 · see citing works

Screen Savers of the World Unite!

Shirts, M., & Pande, V. (2000) · Science · doi:10.1126/science.290.5498.1903 · Cited by 550 · see citing works

Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

Neal, S., Nip, A. M., Zhang, H., & Wishart, D. S. (2003) · Journal of Biomolecular NMR · doi:10.1023/a:1023812930288 · Cited by 540 · see citing works

Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics

Bussi, G., Gervasio, F. L., Laio, A., & Parrinello, M. (2006) · Journal of the American Chemical Society · doi:10.1021/ja062463w · Cited by 507 · see citing works

Determination of Secondary Structure Populations in Disordered States of Proteins Using Nuclear Magnetic Resonance Chemical Shifts

Camilloni, C., Simone, A. D., Vranken, W., & Vendruscolo, M. (2012) · Biochemistry · doi:10.1021/bi3001825 · Cited by 368 · see citing works

Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock–lock mechanism

Nguyen, P. H., Li, M. S., Stock, G., Straub, J. E., & Thirumalai, D. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607440104 · Cited by 355 · see citing works

Reconstructing the equilibrium Boltzmann distribution from well‐tempered metadynamics

Bonomi, M., Barducci, A., & Parrinello, M. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21305 · Cited by 352 · see citing works

Highly Stable Trimers Formed by Human Immunodeficiency Virus Type 1 Envelope Glycoproteins Fused with the Trimeric Motif of T4 Bacteriophage Fibritin

Yang, X., Lee, J., Mahony, E. M., Kwong, P. D., Wyatt, R. T., & Sodroski, J. (2002) · Journal of Virology · doi:10.1128/jvi.76.9.4634-4642.2002 · Cited by 278 · see citing works

Enhanced Sampling in the Well-Tempered Ensemble

Bonomi, M., & Parrinello, M. (2010) · Physical Review Letters · doi:10.1103/physrevlett.104.190601 · Cited by 276 · see citing works

Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding–Binding Process: A Critical Assessment of the “Fly-Casting” Mechanism

Huang, Y., & Liu, Z. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.09.010 · Cited by 266 · see citing works

Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances

Kohlhoff, K., Robustelli, P., Cavalli, A., Salvatella, X., & Vendruscolo, M. (2009) · Journal of the American Chemical Society · doi:10.1021/ja903772t · Cited by 264 · see citing works

Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement

Clore, G. M., Tang, C., & Iwahara, J. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.08.013 · Cited by 226 · see citing works

Structure of bacteriophage T4 fibritin: a segmented coiled coil and the role of the C-terminal domain

Tao, Y. J., Strelkov, S. V., Mesyanzhinov, V. V., & Rossmann, M. G. (1997) · Structure · doi:10.1016/s0969-2126(97)00233-5 · Cited by 224 · see citing works

Stabilization of short collagen-like triple helices by protein engineering

Frank, S., Kammerer, R. A., Mechling, D., Schulthess, T., Landwehr, R., Bann, J., Guo, Y., Lustig, A., Bächinger, H. P., & Engel, J. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4644 · Cited by 213 · see citing works

The courtship of proteins: Understanding the encounter complex

Ubbink, M. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.02.046 · Cited by 176 · see citing works

Foldon, The Natural Trimerization Domain of T4 Fibritin, Dissociates into a Monomeric A-state Form containing a Stable β-Hairpin: Atomic Details of Trimer Dissociation and Local β-Hairpin Stability from Residual Dipolar Couplings

Meier, S., Güthe, S., Kiefhaber, T., & Grzesiek, S. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.09.079 · Cited by 172 · see citing works

Exploring protein aggregation and self‐propagation using lattice models: Phase diagram and kinetics

Dima, R. I., & Thirumalai, D. (2002) · Protein Science · doi:10.1110/ps.4220102 · Cited by 159 · see citing works

Influence of Preformed Asp23−Lys28 Salt Bridge on the Conformational Fluctuations of Monomers and Dimers of Aβ Peptides with Implications for Rates of Fibril Formation

Reddy, G., Straub, J. E., & Thirumalai, D. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp808914c · Cited by 157 · see citing works

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

Deighan, M., Bonomi, M., & Pfaendtner, J. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300297t · Cited by 142 · see citing works

Very Fast Folding and Association of a Trimerization Domain from Bacteriophage T4 Fibritin

Güthe, S., Kapinos, L. E., Möglich, A., Meier, S., Grzesiek, S., & Kiefhaber, T. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.02.020 · Cited by 138 · see citing works

Dynamics and mechanisms of coupled protein folding and binding reactions

Kiefhaber, T., Bachmann, A., & Jensen, K. S. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.09.010 · Cited by 136 · see citing works

Diffusional encounter of barnase and barstar.

Spaar, A., Dammer, C., Gabdoulline, R., Wade, R., & Helms, V. (2006) · Biophysical Journal · doi:10.1529/biophysj.105.075507 · Cited by 119 · see citing works

Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization

Hashimoto, K., Nishi, H., Bryant, S. H., & Panchenko, A. R. (2011) · Physical Biology · doi:10.1088/1478-3975/8/3/035007 · Cited by 110 · see citing works

Replica exchange simulations of transient encounter complexes in protein–protein association

Kim, Y. C., Tang, C., Clore, G. M., & Hummer, G. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802460105 · Cited by 105 · see citing works

Characterization of the Conformational Equilibrium between the Two Major Substates of RNase A Using NMR Chemical Shifts

Camilloni, C., Robustelli, P., Simone, A. D., Cavalli, A., & Vendruscolo, M. (2012) · Journal of the American Chemical Society · doi:10.1021/ja210951z · Cited by 84 · see citing works

Conformational Propensities of Intrinsically Disordered Proteins from NMR Chemical Shifts

Kragelj, J., Ozenne, V., Blackledge, M. J., & Jensen, M. R. (2013) · ChemPhysChem · doi:10.1002/cphc.201300387 · Cited by 79 · see citing works

Linking Well-Tempered Metadynamics Simulations with Experiments

Barducci, A., Bonomi, M., & Parrinello, M. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.01.033 · Cited by 75 · see citing works

Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations

Prakash, M. K., Barducci, A., & Parrinello, M. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct200208h · Cited by 64 · see citing works

Effect of Urea on the β-Hairpin Conformational Ensemble and Protein Denaturation Mechanism

Berteotti, A., Barducci, A., & Parrinello, M. (2011) · Journal of the American Chemical Society · doi:10.1021/ja202849a · Cited by 59 · see citing works

Engineering trimeric fibrous proteins based on bacteriophage T4 adhesins

Анатольевич, М. К., Marusich, E., Cerritelli, M. E., Cheng, N., Hyde, C. C., Steven, A. C., & Mesyanzhinov, V. V. (1998) · Protein Engineering Design and Selection · doi:10.1093/protein/11.4.329 · Cited by 57 · see citing works

Atomistic Description of the Folding of a Dimeric Protein

Piana, S., Lindorff‐Larsen, K., & Shaw, D. E. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp4020993 · Cited by 45 · see citing works

Domain organization, folding and stability of bacteriophage T4 fibritin, a segmented coiled‐coil protein

Boudko, S. P., Londer, Y. Y., Letarov, A. V., Sernova, N. V., Engel, J., & Mesyanzhinov, V. V. (2002) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2002.02734.x · Cited by 36 · see citing works

Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations

Chong, L. T., Snow, C. D., Rhee, Y. M., & Pande, V. S. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.10.083 · Cited by 36 · see citing works

Adenovirus Fibre Shaft Sequences Fold into the Native Triple Beta-Spiral Fold when N-terminally Fused to the Bacteriophage T4 Fibritin Foldon Trimerisation Motif

Papanikolopoulou, K., Teixeira, S. C. M., Belrhali, H., Forsyth, V. T., Mitraki, A., & van Raaij, M. J. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.07.008 · Cited by 32 · see citing works

NMR Structure of a Monomeric Intermediate on the Evolutionarily Optimized Assembly Pathway of a Small Trimerization Domain

Habazettl, J. M., Reiner, A., & Kiefhaber, T. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.03.073 · Cited by 21 · see citing works

Concurrent Association and Folding of Small Oligomeric Proteins

Bosshard, H. R. (2005) · doi:10.1002/9783527619498.ch27 · Cited by 5 · see citing works

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works

Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]

Hénin, J., Tony Lelièvre, A., Shirts, M. R., Valsson, Ó., & Delemotte, L. (2022) · Living Journal of Computational Molecular Science · doi:10.33011/livecoms.4.1.1583 · Cited by 404 · see citing works

Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

Plattner, N., Doerr, S., Fabritiis, G. D., & Noé, F. (2017) · Nature Chemistry · doi:10.1038/nchem.2785 · Cited by 338 · see citing works

Advances in the Simulation of Protein Aggregation at the Atomistic Scale

Carballo‐Pacheco, M., & Strodel, B. (2016) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b00059 · Cited by 125 · see citing works

Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States

Palazzesi, F., Prakash, M. K., Bonomi, M., & Barducci, A. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500718s · Cited by 120 · see citing works

Enhanced sampling techniques in biomolecular simulations

Spiwok, V., Sucur, Z., & Hosek, P. (2014) · Biotechnology Advances · doi:10.1016/j.biotechadv.2014.11.011 · Cited by 110 · see citing works

Artificial intelligence: machine learning for chemical sciences

Karthikeyan, A., & Priyakumar, U. D. (2021) · Journal of Chemical Sciences · doi:10.1007/s12039-021-01995-2 · Cited by 108 · see citing works

Revision of the GROMOS 56A6 CARBO force field: Improving the description of ring‐conformational equilibria in hexopyranose‐based carbohydrates chains

Płaziński, W., Lonardi, A., & Hünenberger, P. H. (2015) · Journal of Computational Chemistry · doi:10.1002/jcc.24229 · Cited by 100 · see citing works

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

Sun, H., Li, Y., Tian, S., Wang, J., & Hou, T. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003729 · Cited by 99 · see citing works

Bacterial Outer Membrane Porins as Electrostatic Nanosieves: Exploring Transport Rules of Small Polar Molecules

Bajaj, H., Acosta‐Gutiérrez, S., Bodrenko, I. V., Malloci, G., Scorciapino, M. A., Winterhalter, M., & Ceccarelli, M. (2017) · ACS Nano · doi:10.1021/acsnano.6b08613 · Cited by 99 · see citing works

The Role of Hydrogen Bonding in the Folding/Unfolding Process of Hydrated Lysozyme: A Review of Recent NMR and FTIR Results

Mallamace, D., Fazio, E., Mallamace, F., & Corsaro, C. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19123825 · Cited by 81 · see citing works

Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics

Zerze, G. H., Miller, C. M., Granata, D., & Mittal, J. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00047 · Cited by 75 · see citing works

Learning free energy landscapes using artificial neural networks

Sidky, H., & Whitmer, J. K. (2018) · The Journal of Chemical Physics · doi:10.1063/1.5018708 · Cited by 63 · see citing works

Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

Lamprakis, C., Andreadelis, I., Manchester, J. I., Velez‐Vega, C., Duca, J. S., & Cournia, Z. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.0c00507 · Cited by 59 · see citing works

Dynamical control by water at a molecular level in protein dimer association and dissociation

Banerjee, P., & Bagchi, B. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1908379117 · Cited by 54 · see citing works

A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations

Martin, J., & Frezza, E. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.970109 · Cited by 54 · see citing works

Unfolding Hidden Barriers by Active Enhanced Sampling

Zhang, J., & Chen, M. (2017) · Physical Review Letters · doi:10.1103/physrevlett.121.010601 · Cited by 41 · see citing works

Dimerization of the EphA1 Receptor Tyrosine Kinase Transmembrane Domain: Insights into the Mechanism of Receptor Activation

Chavent, M. G., Chetwynd, A. P., Stansfeld, P. J., & Sansom, M. S. P. (2014) · Biochemistry · doi:10.1021/bi500800x · Cited by 50 · see citing works

Enhanced sampling of chemical and biochemical reactions with metadynamics

Zheng, S., & Pfaendtner, J. (2014) · Molecular Simulation · doi:10.1080/08927022.2014.923574 · Cited by 46 · see citing works

Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1

Sun, H., Chen, P., Li, D., Li, Y., & Hou, T. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00973 · Cited by 45 · see citing works

An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides

Maffucci, I., & Contini, A. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b01211 · Cited by 45 · see citing works

Enhanced sampling in molecular dynamics simulations and their latest applications—A review

Shen, W., Zhou, T., & Shi, X. (2023) · Nano Research · doi:10.1007/s12274-023-6311-9 · Cited by 44 · see citing works

Melittin Aggregation in Aqueous Solutions: Insight from Molecular Dynamics Simulations

Liao, C., Selvan, M. E., Zhao, J. W., Slimovitch, J. L., Schneebeli, S. T., Shelley, M. Y., Shelley, J. C., & Li, J. (2015) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5b03254 · Cited by 44 · see citing works

Insulin dimer dissociation in aqueous solution: A computational study of free energy landscape and evolving microscopic structure along the reaction pathway

Banerjee, P., Mondal, S., & Bagchi, B. (2018) · The Journal of Chemical Physics · doi:10.1063/1.5042290 · Cited by 42 · see citing works

Coacervation of poly-electrolytes in the presence of lipid bilayers: mutual alteration of structure and morphology

Mondal, S., & Cui, Q. (2022) · Chemical Science · doi:10.1039/d2sc02013k · Cited by 40 · see citing works

Simulation of Reversible Protein–Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints

Perthold, J. W., & Oostenbrink, C. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00706 · Cited by 34 · see citing works

Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: a comparative molecular dynamics simulation study and the underlying mechanisms

Sang, P., Du, X., Yang, L., Meng, Z., & Liu, S.-Q. (2017) · RSC Advances · doi:10.1039/c6ra23230b · Cited by 35 · see citing works

Prion protein β 2– α 2 loop conformational landscape

Caldarulo, E., Barducci, A., Kurt Wüthrich, A., & Parrinello, M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1712155114 · Cited by 32 · see citing works

Molecular modeling study on the dynamical structural features of human smoothened receptor and binding mechanism of antagonist LY2940680 by metadynamics simulation and free energy calculation

Bai, Q., Shen, Y., Jin, N., Liu, H., & Yao, X. (2014) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.03.010 · Cited by 30 · see citing works

Protein Aggregation and Molecular Crowding

Musiani, F., & Giorgetti, A. (2016) · International review of cytology · doi:10.1016/bs.ircmb.2016.08.009 · Cited by 30 · see citing works

Binding Modes of Teixobactin to Lipid II: Molecular Dynamics Study

Liu, Y., Liu, Y., Chan‐Park, M. B. E., & Mu, Y. (2017) · Scientific Reports · doi:10.1038/s41598-017-17606-5 · Cited by 29 · see citing works

αB-crystallin is a sensor for assembly intermediates and for the subunit topology of desmin intermediate filaments

Sharma, S., Conover, G. M., Elliott, J. L., Perng, M. D., Herrmann, H. O., & Quinlan, R. A. (2017) · Cell Stress and Chaperones · doi:10.1007/s12192-017-0788-7 · Cited by 27 · see citing works

Effect of ethanol on insulin dimer dissociation

Banerjee, P., Mondal, S., & Bagchi, B. (2019) · The Journal of Chemical Physics · doi:10.1063/1.5079501 · Cited by 26 · see citing works

Hydrogen Bond Networks and Hydrophobic Effects in the Amyloid β 30–35 Chain in Water: A Molecular Dynamics Study

Jong, K., Grisanti, L., & Hassanali, A. A. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00085 · Cited by 25 · see citing works

Probing oligomerization of amyloid beta peptide in silico

Dorosh, L., & Stepanova, M. (2016) · Molecular BioSystems · doi:10.1039/c6mb00441e · Cited by 25 · see citing works

Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling

Vashisth, H., Skiniotis, G., & Brooks, C. L. (2014) · Chemical Reviews · doi:10.1021/cr4005988 · Cited by 24 · see citing works

ATP Converts Aβ42 Oligomer into Off-Pathway Species by Making Contact with Its Backbone Atoms Using Hydrophobic Adenosine

Kurisaki, I., & Tanaka, S. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.9b07984 · Cited by 24 · see citing works

Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates

Deriu, M. A., Grasso, G., Tuszyński, J. A., Gallo, D., Morbiducci, U., & Danani, A. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004699 · Cited by 23 · see citing works

Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations

Li, L., Casalini, T., Arosio, P., & Salvalaglio, M. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00889 · Cited by 22 · see citing works

Simulation of coupled folding and binding of an intrinsically disordered protein in explicit solvent with metadynamics

Han, M., Xu, J., Ren, Y., & Li, J. (2016) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2016.06.015 · Cited by 22 · see citing works

Exploring Flexibility of Progesterone Receptor Ligand Binding Domain Using Molecular Dynamics

Zheng, L., Lin, V. C. L., & Mu, Y. (2016) · PLoS ONE · doi:10.1371/journal.pone.0165824 · Cited by 21 · see citing works

Molecular mechanisms of 33-mer gliadin peptide oligomerisation

Amundarain, M. J., Herrera, M. G., Zamarreño, F., Viso, J. F., Costabel, M. D., & Dodero, V. I. (2019) · Physical Chemistry Chemical Physics · doi:10.1039/c9cp02338k · Cited by 21 · see citing works

Structural Stability of Insulin Oligomers and Protein Association–Dissociation Processes: Free Energy Landscape and Universal Role of Water

Mukherjee, S., Acharya, S., Mondal, S., Banerjee, P., & Bagchi, B. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c05811 · Cited by 20 · see citing works

Calculating the absolute binding free energy of the insulin dimer in an explicit solvent

Gong, Q., Zhang, H., Zhang, H., & Chen, C. (2020) · RSC Advances · doi:10.1039/c9ra08284k · Cited by 19 · see citing works

Rate of Insulin Dimer Dissociation: Interplay between Memory Effects and Higher Dimensionality

Acharya, S., Mondal, S., Mukherjee, S., & Bagchi, B. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c03779 · Cited by 18 · see citing works

Contribution of Electrostatics in the Fibril Stability of a Model Ionic-Complementary Peptide

Owczarz, M., Casalini, T., Motta, A. C., Morbidelli, M., & Arosio, P. (2015) · Biomacromolecules · doi:10.1021/acs.biomac.5b01092 · Cited by 18 · see citing works

Elucidating Molecular Design Principles for Charge-Alternating Peptides

Smith, J. K., McMullen, P., Yuan, Z., Pfaendtner, J., & Jiang, S. (2019) · Biomacromolecules · doi:10.1021/acs.biomac.9b01191 · Cited by 18 · see citing works

All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors

Mohammadiarani, H., & Vashisth, H. (2016) · Frontiers in Endocrinology · doi:10.3389/fendo.2016.00068 · Cited by 15 · see citing works

Interplay of cysteine exposure and global protein dynamics in small‐molecule recognition by a regulator of G‐protein signaling protein

Mohammadi, M., Mohammadiarani, H., Shaw, V. S., Neubig, R. R., & Vashisth, H. (2018) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25642 · Cited by 14 · see citing works

New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly

Spiga, E., Degiacomi, M. T., & Peraro, M. D. (2014) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2014.06.008 · Cited by 15 · see citing works

GroScore: Accurate Scoring of Protein–Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations

Perthold, J. W., & Oostenbrink, C. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00687 · Cited by 13 · see citing works

Structure-guided design of a trivalent nanobody cluster targeting SARS-CoV-2 spike protein

Jiang, X., Qin, Q., Zhu, H., Qian, J., & Huang, Q. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.128191 · Cited by 13 · see citing works

On the role of residue phosphorylation in 14-3-3 partners: AANAT as a case study

Masone, D., Uhart, M., & Bustos, D. M. (2017) · Scientific Reports · doi:10.1038/srep46114 · Cited by 12 · see citing works

Insulin mimetic peptide S371 folds into a helical structure

Mohammadiarani, H., & Vashisth, H. (2017) · Journal of Computational Chemistry · doi:10.1002/jcc.24746 · Cited by 11 · see citing works

Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method

Han, M., Xu, J., & Ren, Y. (2016) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2016.12.014 · Cited by 11 · see citing works

Counteractive Effects of Choline Geranate (CAGE) ILs and Ethanol on Insulin’s Stability—A Leap Forward towards Oral Insulin Formulation

Palanisamy, K., & Prakash, M. (2022) · Molecules · doi:10.3390/molecules27155031 · Cited by 10 · see citing works

Enhanced Molecular Dynamics Simulations of Intrinsically Disordered Proteins

Masetti, M., Bernetti, M., & Cavalli, A. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0524-0_19 · Cited by 9 · see citing works

General Protein Data Bank-Based Collective Variables for Protein Folding

Ardèvol, A., Palazzesi, F., Tribello, G. A., & Parrinello, M. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00714 · Cited by 8 · see citing works

Computation-aided design of rod-shaped nanoparticles for tumoral targeting

Lee, J., Zhang, W., Nguyen, T. D., Zhou, L., Amengual, J., Zhai, J., Cote, T., Landolina, M., Ahmadi, E., Sands, I., et al. (2025) · Journal of Controlled Release · doi:10.1016/j.jconrel.2025.114169 · Cited by 8 · see citing works

Molecular Dynamics Simulations in Protein–Protein Docking

Cieślak, D., Kabelka, I., & Bartuzi, D. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3985-6_6 · Cited by 8 · see citing works

Reaction Pathway Sampling and Free-Energy Analyses for Multimeric Protein Complex Disassembly by Employing Hybrid Configuration Bias Monte Carlo/Molecular Dynamics Simulation

Kurisaki, I., & Tanaka, S. (2021) · ACS Omega · doi:10.1021/acsomega.0c05579 · Cited by 8 · see citing works

Mechanistic insight into the functional transition of the enzyme guanylate kinase induced by a single mutation

Zhang, Y., Niu, H., Li, Y., Chu, H., Shen, H., Zhang, D., & Li, G. (2015) · Scientific Reports · doi:10.1038/srep08405 · Cited by 7 · see citing works

Thermodynamic Origin of Differential Excipient-Lysozyme Interactions

Kalayan, J., Curtis, R., Warwicker, J., & Henchman, R. H. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.689400 · Cited by 7 · see citing works

New Insights into the Molecular Mechanism of E-Cadherin-Mediated Cell Adhesion by Free Energy Calculations

Doro, F., Saladino, G., Belvisi, L., Civera, M., & Gervasio, F. L. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/ct5010164 · Cited by 6 · see citing works

From Monomers to Hexamers: A Theoretical Probability of the Neighbor Density Approach to Dissect Protein Oligomerization in Cells

Chen, H., & Chen, T. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c04728 · Cited by 5 · see citing works

Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations

Chi, L. A., Asgharpour, S., Correa‐Basurto, J., Bandala, C. R., & Martínez‐Archundia, M. (2022) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-022-00470-5 · Cited by 5 · see citing works

Vector description of electric and hydrophobic interactions in protein homodimers

Mozo-Villarias, Á., Cedano, J. A., & Querol, E. (2015) · European Biophysics Journal · doi:10.1007/s00249-015-1100-3 · Cited by 5 · see citing works

Refining protein structures using enhanced sampling techniques with restraints derived from an ensemble‐based model

Ma, T., Zang, T., Wang, Q., & Ma, J. (2018) · Protein Science · doi:10.1002/pro.3486 · Cited by 4 · see citing works

Optimization of replica exchange temperature ladder under the well-tempered ensemble

Liu, Y., Li, W., & Mu, Y. (2018) · Chemical Physics Letters · doi:10.1016/j.cplett.2018.09.036 · Cited by 4 · see citing works

Applications of enhanced sampling methods to biomolecular self-assembly: a review

Hooten, M., Patel, H., Shao, Y., Singh, R. K., & Dutt, M. (2025) · Journal of Physics Condensed Matter · doi:10.1088/1361-648x/ade650 · Cited by 3 · see citing works

Exploring the structural transition mechanisms of a pair of poly(N-isopropylacrylamide) chains in aqueous solution through coarse-grained molecular simulations coupled with metadynamics

Yang, X., Chen, W., Ren, Y., & Chu, L. (2021) · Molecular Simulation · doi:10.1080/08927022.2021.1881086 · Cited by 3 · see citing works

Advances in missing-in-metastasis research

Lin, X., Cao, M., Gu, N., & Ye, Z. (2015) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/n972014-00981 · Cited by 3 · see citing works

Dimerization and conformation-related free energy landscapes of dye-tagged amyloid-β 12–28 linked to FRET experiments

Kulesza, A. J., Daly, S., & Dugourd, P. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp00611j · Cited by 3 · see citing works

Improving low-accuracy protein structures using enhanced sampling techniques

Zang, T., Ma, T., Wang, Q., & Ma, J. (2018) · The Journal of Chemical Physics · doi:10.1063/1.5027243 · Cited by 3 · see citing works

Conformational ensemble of amyloid-forming semenogelin 1 peptide SEM1(68–107) by NMR spectroscopy and MD simulations

Sanchugova, D., Kusova, A. M., Bikmullin, A. G., Yulmetov, A. R., Mukhametzyanov, T. A., Klochkov, V. V., & Blokhin, D. S. (2022) · Journal of Structural Biology · doi:10.1016/j.jsb.2022.107900 · Cited by 2 · see citing works

Investigation of alanine mutations affecting insulin-like growth factor (IGF) I binding to IGF binding proteins

Chen, X., Duan, D., Zhu, S., & Zhang, J. (2014) · Growth Factors · doi:10.3109/08977194.2014.964868 · Cited by 2 · see citing works

Binding modes of prothrombin cleavage site sequences to the factor Xa catalytic triad: Insights from atomistic simulations

Li, J., Wang, Q., & Tu, Y. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.09.030 · Cited by 2 · see citing works

Hexameric Modules Orchestrate the Hierarchical Pore Assembly of Cytolysin Resolved by Multistack Gel Electrophoresis and Structural Imaging

Liu, M., Song, Y., & Li, X. (2026) · Langmuir · doi:10.1021/acs.langmuir.5c06316 · Cited by 1 · see citing works

Computational and in vitro screening validates the repositioning potential of Coxibs as anti-fibrotic agents

Karande, S., Das, B., Acharya, S. S., Kumar, A., Patel, H., Sharma, A., Gupta, M., Ahmad, I., Bhandare, V. V., Sharma, K., et al. (2024) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2024.2318655 · Cited by 1 · see citing works

Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptidePreprint

Chi, L. A., Asgharpour, S., Correa‐Basurto, J., Bandala, C., & Martínez‐Archundia, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.23.493150 · Cited by 1 · see citing works

Exploring Energy Profiles of Protein-Protein Interactions (PPIs) Using DFT Method

Bapat, S., Vyas, R., & Karthikeyan, M. (2018) · Letters in Drug Design & Discovery · doi:10.2174/1570180815666180815151141

Modelling the structure and interactions of intrinsically disordered proteins with multiple-replica, metadynamics-based sampling methods and force-field combinationsPreprint

Li, L., Casalini, T., Arosio, P., & Salvalaglio, M. (2021) · doi:10.33774/chemrxiv-2021-4gg4g-v2

Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinationsPreprint

Li, L., Casalini, T., Arosio, P., & Salvalaglio, M. (2021) · ChemRxiv · doi:10.26434/chemrxiv-2021-4gg4g

Kinetics and Thermodynamics of Protein–Protein Encounter

Künzel, N., & Helms, V. (2022) · Wiley eBooks · doi:10.1002/9783527830503.ch8

Mechanism of Phosphatidylserine Lipid Scrambling by Human SERINC3, an HIV-1 Restriction FactorPreprint

Banerjee, P., Yeager, M. J., & Voth, G. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.13.688349

Development of predictive approaches for biomolecular association kinetics

Palacio‐Rodríguez, K. (2022) · doi:10.70675/7bce36a3zf761z41b4z8daaz3e5e7740dc71

Spatial and electronic structure of proteins

Yang, Z., Zhao, D., & Liu, C. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-44921-5.00019-5

NMR Structure of a Monomeric Intermediate on the Evolutionarily Optimized Assembly Pathway of a Small Trimerization Domain

Habazettl, J. M., Reiner, A., & Kiefhaber, T. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.03.073 · Cited by 21 · see citing works

Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations

Chong, L. T., Snow, C. D., Rhee, Y. M., & Pande, V. S. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.10.083 · Cited by 36 · see citing works

Multiscale molecular dynamics studies of peptide aggregation and protein-ligand association

Magno, A. (2013) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-92921

Atomistic molecular simulations of protein folding

Best, R. B. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.12.001 · Cited by 139 · see citing works

Predictive energy landscapes for folding membrane protein assemblies

Truong, H. H., Kim, B. L., Schafer, N. P., & Wolynes, P. G. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4929598 · Cited by 14 · see citing works