AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Computer Simulation of Liquids

Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945

The Amber biomolecular simulation programs

Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535

The General Utility Lattice Program ( GULP )

Gale, J. D., & Rohl, A. L. (2003) · Molecular Simulation · doi:10.1080/0892702031000104887 · Cited by 2,265

Reaction coordinates of biomolecular isomerization

Bolhuis, P. G., Dellago, C., & Chandler, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.100127697 · Cited by 426

Automatic Method for Identifying Reaction Coordinates in Complex Systems

Ma, A., & Dinner, A. R. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045546c · Cited by 400

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

Potapov, V., Cohen, M., & Schreiber, G. (2009) · Protein Engineering Design and Selection · doi:10.1093/protein/gzp030 · Cited by 349

Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

Muller, M. P., Jiang, T., Sun, C., Lihan, M., Pant, S., Mahinthichaichan, P., Trifan, A., & Tajkhorshid, E. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00608 · Cited by 282

Molecular basis of RNA recognition by the human alternative splicing factor Fox-1

Auweter, S. D., Fasan, R., Reymond, L., Underwood, J. G., Black, D. L., Pitsch, S., & Allain, F. H. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7600918 · Cited by 264

Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations

Abrams, J. B., & Tuckerman, M. E. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp805039u · Cited by 221

Therapeutic Inhibition of Myc in Cancer. Structural Bases and Computer-Aided Drug Discovery Approaches

Carabet, L. A., Rennie, P. S., & Cherkasov, A. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms20010120 · Cited by 172

Transient binding of an activator BH3 domain to the Bak BH3-binding groove initiates Bak oligomerization

Dai, H., Smith, A., Meng, X. W., Schneider, P. A., Pang, Y.-P., & Kaufmann, S. H. (2011) · Journal of Cell Biology · doi:10.1083/jcb.201102027 · Cited by 159

Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules

Tuszyński, J. A., Brown, J. A., Crawford, E., Carpenter, E. J., Nip, M. L. A., Dixon, J. M., & Satarić, M. V. (2005) · Mathematical and Computer Modelling · doi:10.1016/j.mcm.2005.05.002 · Cited by 124

Modelling biological complexity: a physical scientist's perspective

Coveney, P. V., & Fowler, P. W. (2005) · Journal of The Royal Society Interface · doi:10.1098/rsif.2005.0045 · Cited by 117

Coarse graining of short polythylene chains for studying polymer crystallization

Vettorel, T., & Meyer, H. (2006) · Journal of Chemical Theory and Computation · doi:10.1021/ct0503264 · Cited by 90

Structural and Functional Impact of Parkinson Disease-Associated Mutations in the E3 Ubiquitin Ligase Parkin: HUMAN MUTATION

Fiesel, F. C., Caulfield, T. R., Moussaud-Lamodière, E. L., Ogaki, K., Dourado, D. F. A. R., Flores, S. C., Ross, O. A., & Springer, W. (2015) · Human Mutation · doi:10.1002/humu.22808 · Cited by 89

Computational predictions of volatile anesthetic interactions with the microtubule cytoskeleton: implications for side effects of general anesthesia

Craddock, T. J. A., St. George, M., Freedman, H., Barakat, K. H., Damaraju, S., Hameroff, S., & Tuszynski, J. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037251 · Cited by 84

Integrative structure modeling of macromolecular assemblies from proteomics data

Lasker, K., Phillips, J. L., Russel, D., Velázquez-Muriel, J., Schneidman-Duhovny, D., Tjioe, E., Webb, B., Schlessinger, A., & Sali, A. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r110.000067 · Cited by 71

All Wired Up: An Exploration of the Electrical Properties of Microtubules and Tubulin

Kalra, A. P., Eakins, B. B., Patel, S. D., Ciniero, G., Rezania, V., Shankar, K., & Tuszynski, J. A. (2020) · ACS Nano · doi:10.1021/acsnano.0c06945 · Cited by 49

Structure and dynamics of Cu(I) binding in copper chaperones Atox1 and CopZ: a computer simulation study.

Rodriguez-Granillo, A., & Wittung-Stafshede, P. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp711787x · Cited by 39

Proton Transfer in Guanine-Cytosine Base Pairs in B-DNA

Soler-Polo, D., Mendieta-Moreno, J. I., Trabada, D. G., Mendieta, J., & Ortega, J. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b00757 · Cited by 38

Probing the Tryptophan Environment in Therapeutic Proteins: Implications for Higher Order Structure on Tryptophan Oxidation

Barnett, G. V., Balakrishnan, G., Chennamsetty, N., Hoffman, L., Bongers, J., Tao, L., Huang, Y., Slaney, T., Das, T. K., Leone, A., et al. (2019) · Journal of Pharmaceutical Sciences · doi:10.1016/j.xphs.2018.12.027 · Cited by 33

Solution structure of the N‐terminal catalytic domain of human H‐REV107 – A novel circular permutated NlpC/P60 domain

Ren, X., Lin, J., Jin, C., & Xia, B. (2010) · FEBS Letters · doi:10.1016/j.febslet.2010.09.015 · Cited by 29

Viro3D: a comprehensive database of virus protein structure predictions

(2025) · doi:10.1038/s44320-025-00147-9 · Cited by 28

Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities

Pham, G. H., Rana, A. S. J. B., Korkmaz, E. N., Trang, V. H., Cui, Q., & Strieter, E. R. (2016) · Protein Science · doi:10.1002/pro.2834 · Cited by 21

Charge Effects on the Fibril-Forming Peptide KTVIIE: A Two-Dimensional Replica Exchange Simulation Study

Jeon, J., & Shell, M. S. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.03.019 · Cited by 16

The measured and calculated affinity of methyl‐ and methoxy‐substituted benzoquinones for the QAsite of bacterial reaction centers

Zheng, Z., Dutton, P. L., & Gunner, M. R. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22779 · Cited by 13

Can Peptide Folding Simulations Provide Predictive Information for Aggregation Propensity?

Lin, E. I., & Shell, M. S. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp104114n · Cited by 12

Chatbot-assisted quantum chemistry for explicitly solvated molecules

(2025) · doi:10.1039/d4sc08677e · Cited by 11

Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations

Sadiq, S. K., Muñiz Chicharro, A., Friedrich, P., & Wade, R. C. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00673 · Cited by 8

Lethal events in V79 cells irradiated by low-energy protons and correlations with distribution patterns of energy deposition, radical concentration and DNA damage

Davídková, M., Kundrát, P., Štěpán, V., Palajová, Z., & Judas, L. (2009) · Applied Radiation and Isotopes · doi:10.1016/j.apradiso.2008.06.035 · Cited by 7

Atomic-Resolution Prediction of Degrader-mediated Ternary Complex Structures by Combining Molecular Simulations with Hydrogen Deuterium Exchange

Dixon, T., MacPherson, D., Mostofian, B., Dauzhenka, T., Lotz, S., McGee, D., Shechter, S., Shrestha, U. R., Wiewiora, R., McDargh, Z. A., et al. (2021) · doi:10.1101/2021.09.26.461830 · Cited by 7