Force Fields for Protein Simulations

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 Protein-Folding Problem, 50 Years On

Dill, K. A., & MacCallum, J. L. (2012) · Science · doi:10.1126/science.1219021 · Cited by 1,699

Current Status of the AMOEBA Polarizable Force Field

Ponder, J. W., Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., Lambrecht, D. S., DiStasio, R. A., et al. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp910674d · Cited by 1,440

To milliseconds and beyond: challenges in the simulation of protein folding

Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.11.002 · Cited by 409

Progress in Modeling of Protein Structures and Interactions.

Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., & Baker, D. (2005) · Science · doi:10.1126/science.1112160 · Cited by 294

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

TorchMD: A Deep Learning Framework for Molecular Simulations

Doerr, S., Majewski, M., Pérez, A., Krämer, A., Clementi, C., Noe, F., Giorgino, T., & De Fabritiis, G. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.0c01343 · Cited by 230

Quantum Computing for Molecular Biology**

Baiardi, A., Christandl, M., & Reiher, M. (2023) · ChemBioChem · doi:10.1002/cbic.202300120 · Cited by 93

Biomolecular simulation and modelling: status, progress and prospects

van der Kamp, M. W., Shaw, K. E., Woods, C. J., & Mulholland, A. J. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0105.focus · Cited by 90

Antibody H3 structure prediction

Marks, C., & Deane, C. M. (2017) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2017.01.010 · Cited by 56

Robust scoring functions for protein-ligand interactions with quantum chemical charge models.

Wang, J.-C., Lin, J.-H., Chen, C.-M., Perryman, A. L., & Olson, A. J. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200220v · Cited by 54

A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models

Baiz, C. R., Lin, Y.-S., Peng, C. S., Beauchamp, K. A., Voelz, V. A., Pande, V. S., & Tokmakoff, A. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.02.008 · Cited by 51

From Membrane Composition to Antimicrobial Strategies: Experimental and Computational Approaches to AMP Design and Selectivity

Rossetti, P., Trollmann, M. F. W., Wichmann, C., Gutsmann, T., Eggeling, C., & Böckmann, R. A. (2026) · Small · doi:10.1002/smll.202411476 · Cited by 25

Consensus in silico computational modelling of the p22phox subunit of the NADPH oxidase

Meijles, D. N., Howlin, B. J., & Li, J.-M. (2012) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2012.05.001 · Cited by 22

Vibrio cholerae’s ToxRS bile sensing system

Gubensäk, N., Sagmeister, T., Buhlheller, C., Geronimo, B. D., Wagner, G. E., Petrowitsch, L., Gräwert, M. A., Rotzinger, M., Berger, T. M. I., Schäfer, J., et al. (2023) · eLife · doi:10.7554/elife.88721 · Cited by 14

Thermodynamic Stability and Flexibility Characteristics of Antibody Fragment Complexes

Li, T., Verma, D., Tracka, M., Casas-Finet, J., Livesay, D., & Jacobs, D. (2013) · Protein & Peptide Letters · doi:10.2174/09298665113209990051 · Cited by 13

Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2

Zhu, C., Cao, S., Shang, T., Guo, J., Su, A., Li, C., & Duan, H. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf202 · Cited by 13

Investigating the Structural Origin of Trpzip2 Temperature Dependent Unfolding Fluorescence Line Shape Based on a Markov State Model Simulation

Song, J., Gao, F., Cui, R. Z., Shuang, F., Liang, W., Huang, X., & Zhuang, W. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp304714q · Cited by 10

AP2/ERF Transcription Factor Orthologs of the Desert Tree Prosopis cineraria Show Higher Copy Number and DNA-Binding Affinity than Drought-Sensitive Species

(2024) · doi:10.1007/s00344-024-11532-3 · Cited by 3

Multiscale computational analysis reveals enhanced allosteric modulation of Nav1.5 by dual binding of dapagliflozin and ertugliflozin

Chattopadhyay, A., Fatehi, M., Mosa, F. E. S., Gruber, B., Light, P. E., & Barakat, K. (2025) · Scientific Reports · doi:10.1038/s41598-025-30298-6 · Cited by 2