GROMACS: A message-passing parallel molecular dynamics implementation

‘GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers’

Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015) · SoftwareX · doi:10.1016/j.softx.2015.06.001 · Cited by 27,190

Scalable molecular dynamics with NAMD

Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914

Potential for biomolecular imaging with femtosecond X-ray pulses

Neutze, R., Wouts, R., van der Spoel, D., Weckert, E., & Hajdu, J. (2000) · Nature · doi:10.1038/35021099 · Cited by 2,022

Cell-cycle dynamics of chromosomal organization at single-cell resolution

Nagano, T., Lubling, Y., Várnai, C., Dudley, C., Leung, W., Baran, Y., Mendelson Cohen, N., Wingett, S., Fraser, P., & Tanay, A. (2017) · Nature · doi:10.1038/nature23001 · Cited by 794

Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor

Yang, J., Petitjean, S. J. L., Koehler, M., Zhang, Q., Dumitru, A. C., Chen, W., Derclaye, S., Vincent, S. P., Soumillion, P., & Alsteens, D. (2020) · Nature Communications · doi:10.1038/s41467-020-18319-6 · Cited by 615

Almost all about citrulline in mammals

Curis, E., Nicolis, I., Moinard, C., Osowska, S., Zerrouk, N., Bénazeth, S., & Cynober, L. (2005) · Amino Acids · doi:10.1007/s00726-005-0235-4 · Cited by 571

Mutation of the RAD51C gene in a Fanconi anemia–like disorder

Vaz, F., Hanenberg, H., Schuster, B., Barker, K., Wiek, C., Erven, V., Neveling, K., Endt, D., Kesterton, I., Autore, F., et al. (2010) · Nature Genetics · doi:10.1038/ng.570 · Cited by 408

Progress and challenges in the automated construction of Markov state models for full protein systems

Bowman, G. R., Beauchamp, K. A., Boxer, G., & Pande, V. S. (2009) · The Journal of Chemical Physics · doi:10.1063/1.3216567 · Cited by 396

Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations

Harmandaris, V. A., Adhikari, N. P., van der Vegt, N. F. A., & Kremer, K. (2006) · Macromolecules · doi:10.1021/ma0606399 · Cited by 350

Predicting free energy changes using structural ensembles

Benedix, A., Becker, C. M., de Groot, B. L., Caflisch, A., & Böckmann, R. A. (2009) · Nature Methods · doi:10.1038/nmeth0109-3 · Cited by 234

Structural and Functional Characterization of the Aryl Hydrocarbon Receptor Ligand Binding Domain by Homology Modeling and Mutational Analysis

Pandini, A., Denison, M. S., Song, Y., Soshilov, A. A., & Bonati, L. (2007) · Biochemistry · doi:10.1021/bi061460t · Cited by 160

Microstructure of Catalyst Layers in PEM Fuel Cells Redefined: A Computational Approach

Malek, K., Mashio, T., & Eikerling, M. (2011) · Electrocatalysis · doi:10.1007/s12678-011-0047-0 · Cited by 151

Osmolyte Trimethylamine-N-Oxide Does Not Affect the Strength of Hydrophobic Interactions: Origin of Osmolyte Compatibility

Athawale, M. V., Dordick, J. S., & Garde, S. (2005) · Biophysical Journal · doi:10.1529/biophysj.104.056671 · Cited by 153

Molecular-Basis of Single-Walled Carbon Nanotube Recognition by Single-Stranded DNA

Roxbury, D., Mittal, J., & Jagota, A. (2012) · Nano Letters · doi:10.1021/nl204182b · Cited by 137

Accelerating the prediction and discovery of peptide hydrogels with human-in-the-loop

Xu, T., Wang, J., Zhao, S., Chen, D., Zhang, H., Fang, Y., Kong, N., Zhou, Z., Li, W., & Wang, H. (2023) · Nature Communications · doi:10.1038/s41467-023-39648-2 · Cited by 132

Detection of the TCDD Binding-Fingerprint within the Ah Receptor Ligand Binding Domain by Structurally Driven Mutagenesis and Functional Analysis

Pandini, A., Soshilov, A. A., Song, Y., Zhao, J., Bonati, L., & Denison, M. S. (2009) · Biochemistry · doi:10.1021/bi900259z · Cited by 124

Thermodynamic forces from protein and water govern condensate formation of an intrinsically disordered protein domain

(2023) · doi:10.1038/s41467-023-41586-y · Cited by 118

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

Activation-triggered subunit exchange between CaMKII holoenzymes facilitates the spread of kinase activity

Stratton, M., Lee, I.-H., Bhattacharyya, M., Christensen, S. M., Chao, L. H., Schulman, H., Groves, J. T., & Kuriyan, J. (2014) · eLife · doi:10.7554/elife.01610 · Cited by 114

Potential neutralizing antibodies discovered for novel corona virus using machine learning

Magar, R., Yadav, P., & Barati Farimani, A. (2021) · Scientific Reports · doi:10.1038/s41598-021-84637-4 · Cited by 114

Molecular mechanism of activation-triggered subunit exchange in Ca2+/calmodulin-dependent protein kinase II

Bhattacharyya, M., Stratton, M. M., Going, C. C., McSpadden, E. D., Huang, Y., Susa, A. C., Elleman, A., Cao, Y. M., Pappireddi, N., Burkhardt, P., et al. (2016) · eLife · doi:10.7554/elife.13405 · Cited by 112

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

Lin, Y.-S., Bowman, G. R., Beauchamp, K. A., & Pande, V. S. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2011.12.002 · Cited by 111

From mesoscale back to atomistic models: A fast reverse-mapping procedure for vinyl polymer chains

Santangelo, G., Di Matteo, A., Müller-Plathe, F., & Milano, G. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp066212l · Cited by 104

Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation.

Allen, W. J., Corey, R. A., Oatley, P., Sessions, R. B., Baldwin, S. A., Radford, S. E., Tuma, R., & Collinson, I. (2016) · eLife · doi:10.7554/elife.15598 · Cited by 103

Predicting polymer dynamics at multiple length and time scales

Harmandaris, V. A., & Kremer, K. (2009) · Soft Matter · doi:10.1039/b905361a · Cited by 90

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

Topological entanglement length in polymer melts and nanocomposites by a DPD polymer model

Karatrantos, A., Clarke, N., Composto, R. J., & Winey, K. I. (2013) · Soft Matter · doi:10.1039/c3sm27651a · Cited by 76

Computational enzyme design by catalytic motif scaffolding

Braun, M., Tripp, A., Chakatok, M., Kaltenbrunner, S., Fischer, C., Stoll, D., Bijelic, A., Elaily, W., Totaro, M. G., Moser, M., et al. (2026) · Nature · doi:10.1038/s41586-025-09747-9 · Cited by 73

Identification of Nicotinamide Mononucleotide Deamidase of the Bacterial Pyridine Nucleotide Cycle Reveals a Novel Broadly Conserved Amidohydrolase Family

Galeazzi, L., Bocci, P., Amici, A., Brunetti, L., Ruggieri, S., Romine, M., Reed, S., Osterman, A. L., Rodionov, D. A., Sorci, L., et al. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.275818 · Cited by 67

Interactions of the Calcite {10.4} Surface with Organic Compounds: Structure and Behaviour at Mineral – Organic Interfaces

Hakim, S. S., Olsson, M. H. M., Sørensen, H. O., Bovet, N., Bohr, J., Feidenhans’l, R., & Stipp, S. L. S. (2017) · Scientific Reports · doi:10.1038/s41598-017-06977-4 · Cited by 66

Structural Characteristics of Oligomeric DNA Strands Adsorbed onto Single-Walled Carbon Nanotubes

Roxbury, D., Jagota, A., & Mittal, J. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp309523a · Cited by 59

RGD delivery of truncated coagulase to tumor vasculature affords local thrombotic activity to induce infarction of tumors in mice

Jahanban-Esfahlan, R., Seidi, K., Monhemi, H., Adli, A. D. F., Minofar, B., Zare, P., Farajzadeh, D., Farajnia, S., Behzadi, R., Abbasi, M. M., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-05326-9 · Cited by 58

Insights from incorporating quantum computing into drug design workflows

Lau, B., Emani, P. S., Chapman, J., Yao, L., Lam, T., Merrill, P., Warrell, J., Gerstein, M. B., & Lam, H. Y. K. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btac789 · Cited by 54

Entanglements and dynamics of polymer melts near a SWCNT

Karatrantos, A., Composto, R. J., Winey, K. I., Kröger, M., & Clarke, N. (2012) · Macromolecules · doi:10.1021/ma3007637 · Cited by 53

Experimental and molecular dynamics simulation study of specific ion effect on the graphene oxide surface and investigation of the influence on reactive extraction of model dye molecule at water–organic interface

Borthakur, P., Boruah, P. K., Hussain, N., Sharma, B., Das, M. R., Matić, S., Řeha, D., & Minofar, B. (2016) · The Journal of Physical Chemistry C · doi:10.1021/acs.jpcc.6b02787 · Cited by 49

Combined x-ray crystallography and computational modeling approach to investigate the Hsp90 C-terminal peptide binding to FKBP51

Kumar, R., Moche, M., Winblad, B., & Pavlov, P. F. (2017) · Scientific Reports · doi:10.1038/s41598-017-14731-z · Cited by 40

Adsorption of Ethanol and Water on Calcite: Dependence on Surface Geometry and Effect on Surface Behavior

Keller, K. S., Olsson, M. H. M., Yang, M., & Stipp, S. L. S. (2015) · Langmuir · doi:10.1021/la504319z · Cited by 39

Backmapping coarse-grained polymer models under sheared nonequilibrium conditions

Chen, X., Carbone, P., Santangelo, G., Di Matteo, A., Milano, G., & Müller-Plathe, F. (2009) · Physical Chemistry Chemical Physics · doi:10.1039/b817895j · Cited by 34

Structural and Functional Influence of the Glycine-Rich Loop G 302 GGGY on the Catalytic Tyrosine of Histone Deacetylase 8

Porter, N. J., Christianson, N. H., Decroos, C., & Christianson, D. W. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b01014 · Cited by 33

Conformational distributions of isolated myosin motor domains encode their mechanochemical properties

Porter, J. R., Meller, A., Zimmerman, M. I., Greenberg, M. J., & Bowman, G. R. (2020) · eLife · doi:10.7554/elife.55132 · Cited by 31

ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery.

Corey, R. A., Ahdash, Z., Shah, A., Pyle, E., Allen, W. J., Fessl, T., Lovett, J. E., Politis, A., & Collinson, I. (2019) · eLife · doi:10.7554/elife.41803 · Cited by 30

Molecular Dynamics Simulations, Solvatochromic Parameters, and Preferential Solvation in Aqueous Solutions of Ethaline, Ethylene Glycol, and Choline Chloride

Aryafard, M., Karimi, A., Harifi-Mood, A. R., & Minofar, B. (2020) · Journal of Chemical & Engineering Data · doi:10.1021/acs.jced.0c00381 · Cited by 29

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles

Conev, A., Rigo, M. M., Devaurs, D., Fonseca, A. F., Kalavadwala, H., de Freitas, M. V., Clementi, C., Zanatta, G., Antunes, D. A., & Kavraki, L. E. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad242 · Cited by 28

Palbociclib can overcome mutations in cyclin dependent kinase 6 that break hydrogen bonds between the drug and the protein

Hernandez Maganhi, S., Jensen, P., Caracelli, I., Zukerman Schpector, J., Fröhling, S., & Friedman, R. (2017) · Protein Science · doi:10.1002/pro.3135 · Cited by 25

Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI

Schindler, C. E. M., Chauvot de Beauchêne, I., de Vries, S. J., & Zacharias, M. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25196 · Cited by 20

Drug Target Prioritization for Alzheimer's Disease Using Protein Interaction Network Analysis

Podder, A., Pandit, M., & Narayanan, L. (2018) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2018.0131 · Cited by 14

Structural and functional analysis of vaccinia viral fusion complex component protein A28 through NMR and molecular dynamic simulations

Kao, C.-F., Tsai, M.-H., Carillo, K. J., Tzou, D.-L., & Chang, W. (2023) · PLOS Pathogens · doi:10.1371/journal.ppat.1011500 · Cited by 13

Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost

(2024) · doi:10.1002/pro.5239 · Cited by 12

Role of Intrinsically Disordered Regions in Acceleration of Protein–Protein Association

Misiura, M. M., & Kolomeisky, A. B. (2020) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.9b08793 · Cited by 10

Explaining the interaction of mangiferin with MMP-9 and NF-ƙβ: a computational study

Gálvez-Rodríguez, A., Ferino-Pérez, A., Rodríguez-Riera, Z., Rodeiro Guerra, I., Řeha, D., Minofar, B., & Jáuregui-Haza, U. J. (2022) · Journal of Molecular Modeling · doi:10.1007/s00894-022-05260-2 · Cited by 9

Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD)

Deganutti, G., Pipito, L., Rujan, R. M., Weizmann, T., Griffin, P., Ciancetta, A., Moro, S., & Reynolds, C. A. (2025) · eLife · doi:10.7554/elife.96513 · Cited by 7

Computational Approaches to Zeolite-Based Adsorption Processes

Gutiérrez-Sevillano, J. J., & Calero, S. (2020) · Structure and Bonding · doi:10.1007/430_2020_66 · Cited by 4

Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation

Quintana-Feliciano, R., Kottur, J., Ni, M., Ghosh, R., Salas-Estrada, L., Ahlsen, G., Rechkoblit, O., Shapiro, L., Filizola, M., Fang, G., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52130-x · Cited by 3

Harnessing Photosynthetic ATP for Whole-Cell Biocatalysis in the Cyanobacterium Synechocystis

Loprete, G., Traverso, E., Vascon, F., Botteri, M., Robescu, M. S., Ubiali, D., Cendron, L., Morosinotto, T., & Bergantino, E. (2025) · ACS Sustainable Chemistry & Engineering · doi:10.1021/acssuschemeng.5c07236 · Cited by 2

Correlating membrane‐protein dynamics with function: Integrating bioinformatics, molecular dynamics, and single‐molecule FRET

Higinbotham, H. R., Arbour, C. A., & Imperiali, B. (2025) · Protein Science · doi:10.1002/pro.70352 · Cited by 2

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

Computational design of Bax-inhibiting peptides

Vlaar, T., Mayer, B., van der Heide, L., & Ilie, I. M. (2025) · Materials Advances · doi:10.1039/d4ma01142b · Cited by 2

Structural characterization of DNA-binding domain of essential mammalian protein TTF 1

Singh, G., Bhopale, A. J., Khatri, S., Prakash, P., Kumar, R., Singh, S. M., & Singh, S. K. (2024) · Bioscience Reports · doi:10.1042/bsr20240800 · Cited by 1

A computational model for lipid-anchored polysaccharide export by the outer membrane protein GfcD

Fruet, C., Martinez-Goikoetxea, M., Merino, F., & Lupas, A. N. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2024.08.012 · Cited by 1

Conformational distributions of isolated myosin motor domains encode their mechanochemical properties

Porter, J. R., Meller, A., Zimmerman, M. I., Greenberg, M. J., & Bowman, G. R. (2019) · doi:10.1101/2019.12.16.878264