The DOI matches its Crossref record; 54 of the 55 references it cites were found in a registry or an index.
Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Methods such as MM-PBSA and MM-GBSA,46,47 which are based on molecular dynamics (MD) simulations, offer an alternative route for computing the binding free energies of protein–protein systems48−50 including coiled-coil complexes.42,51,52”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [47]
Citations
Cites
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
Darden, T., York, D., & Pedersen, L. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464397 · Cited by 29,638
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00124a002 · Cited by 13,111
Self-citationKlamt, A., & Schüürmann, G. (1993) · Journal of the Chemical Society Perkin Transactions 2 · doi:10.1039/p29930000799 · Cited by 9,449
Bayly, C. I., Cieplak, P., Cornell, W. D., & Kollman, P. A. (1993) · The Journal of Physical Chemistry · doi:10.1021/j100142a004 · Cited by 8,152
Self-citationTomasi, J., & Persico, M. (1994) · Chemical Reviews · doi:10.1021/cr00031a013 · Cited by 5,530
Electric Moments of Molecules in Liquids
Onsager, L. (1936) · Journal of the American Chemical Society · doi:10.1021/ja01299a050 · Cited by 5,350
Semianalytical treatment of solvation for molecular mechanics and dynamics
Still, W. C., Tempczyk, A., Hawley, R. C., & Hendrickson, T. F. (1990) · Journal of the American Chemical Society · doi:10.1021/ja00172a038 · Cited by 3,653
Classical Electrostatics in Biology and Chemistry
Honig, B. H., & Nicholls, A. O. (1995) · Science · doi:10.1126/science.7761829 · Cited by 2,891
Miertuš, S., & Tomasi, J. (1982) · Chemical Physics · doi:10.1016/0301-0104(82)85072-6 · Cited by 2,480
Research works printed but not linked: 4
- Born, M.Z., Phys., 1 (1920) 45.
- Debye, P. and Hückel, E., Physik. Z., 24 (1923) 185.
- Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.R., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P. and Kollman, P.A., AMBER4.1 (UCSF), University of California, San Francisco, CA, 1995.
- Jorgensen, W.L., BOSS3.6, Yale University, New Haven, CT, 1996.
Cited by
Sorted by citations
Items 501–600 of 1,000
Zhang, X., Wang, Y., Wang, H., Li, H., Zhang, T., Peng, Y., & Wang, X. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b01040 · Cited by 14
Wei, X., Zhang, L., Zhang, R., Wu, R., Si, D., Ahmad, B., Petitte, J. N., Mozdziak, P. E., Li, Z., Guo, H., et al. (2020) · The FASEB Journal · doi:10.1096/fj.201903263rrr · Cited by 14
Liu, X., Wang, Z., Gao, Y., Liu, C., Wang, J., Li, F., Min, W., & Zhang, J. (2021) · Physical Chemistry Chemical Physics · doi:10.1039/d1cp00172h · Cited by 14
Molecular Mechanisms of the Blockage of Glioblastoma Motility
Xu, J., Simonelli, F., Li, X., Spinello, A., Laporte, S., Torre, V., & Magistrato, A. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00279 · Cited by 14
Molecular Dynamics Simulation Study on Stabilities and Reactivities of NADH Cytochrome B5 Reductase
Asada, T., Nagase, S., Nishimoto, K., & Koseki, S. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp7101513 · Cited by 14
Almatary, A. M., Al-Sanea, M. M., Nasr, E. E., Haikal, A., Thompson, G. S., Abood, A., Ibrahim, M. A. A., Elgazar, A. A., & Hamdi, A. (2025) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2025.108295 · Cited by 13
In silico evaluation of lapachol derivatives binding to the Nsp9 of SARS-CoV-2
Nicolau-Júnior, N., Santos, I. A., Meireles, B. A., Nicolau, M. S. P., Lapa, I. R., Aguiar, R. S., Jardim, A. C. G., & José, D. P. (2021) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2021.1875050 · Cited by 13
Mtambo, S. E., & Kumalo, H. M. (2022) · Molecules · doi:10.3390/molecules27144515 · Cited by 13
Jha, V., Holmelin, F. L., & Eriksson, L. A. (2023) · ACS Omega · doi:10.1021/acsomega.2c08025 · Cited by 13
Solvated interaction energy: from small-molecule to antibody drug design
Purisima, E. O., Corbeil, C. R., Gaudreault, F., Wei, W., Deprez, C., & Sulea, T. I. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1210576 · Cited by 14
An allosteric mechanism for potent inhibition of SARS-CoV-2 main proteinase
Zhang, Y., Guo, J., Liu, Y., Qu, Y., Li, Y., Mu, Y., & Li, W. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.130644 · Cited by 13
In silico fragment-based discovery of CIB1-directed anti-tumor agents by FRASE-bot
An, Y., Lim, J., Glavatskikh, M., Wang, X., Norris-Drouin, J. L., Hardy, P. B., Leisner, T. M., Pearce, K. H., & Kireev, D. (2024) · Nature Communications · doi:10.1038/s41467-024-49892-9 · Cited by 12
Chaurasia, S., Pieraccini, S., Gonda, R. D., Conti, S., & Sironi, M. (2013) · Chemical Physics Letters · doi:10.1016/j.cplett.2013.09.042 · Cited by 12
Navrátilová, V., Paloncýová, M., Berka, K., Mise, S., Haga, Y., Matsumura, C., Sakaki, T., Inui, H., & Otyepka, M. (2017) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2017.08.002 · Cited by 13
Prospective new amidinothiazoles as leukotriene B4 inhibitors
Aly, A. A., Ibrahim, M. A. A., El‐Sheref, E. M., Hassan, A. M. A., & Brown, A. B. (2018) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2018.07.085 · Cited by 14
Luo, A., Li, X., Zhang, X., Zhan, H., Du, H., Zhang, Y., & Peng, X. (2019) · Royal Society Open Science · doi:10.1098/rsos.190219 · Cited by 13
Prabhudesai, K. S., Raje, S., Dhamanaskar, A., Modi, D. N., Dighe, V. D., Contini, A., & Idicula‐Thomas, S. (2020) · Peptides · doi:10.1016/j.peptides.2020.170367 · Cited by 13
Ji, B., Xue, Y., Xu, Y., Liu, S., Gough, A., Xie, X., & Wang, J. (2021) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.0c00810 · Cited by 14
Liu, X., Zheng, L., Qin, C., Cong, Y., Zhang, J. Z. H., & Sun, Z. (2023) · Molecules · doi:10.3390/molecules28062767 · Cited by 13
Moonsamy, S., Bhakat, S., Ramesh, M., & Soliman, M. E. S. (2016) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-016-0774-1 · Cited by 13
Fluorinated PET Tracers for Molecular Imaging of σ1 Receptors in the Central Nervous System
Weber, F., Brust, P., Laurini, E., Pricl, S., & Wünsch, B. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-50174-1_4 · Cited by 13
Wang, J., Chen, Q., Wang, M., & Zhong, C. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp03443a · Cited by 13
Modeling caspase-1 inhibition: Implications for catalytic mechanism and drug design
Ramos‐Guzmán, C. A., Zinovjev, K., & Tuñón, I. (2019) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2019.02.064 · Cited by 13
Yan, F., Liu, X., Zhang, S., Zhang, Q., & Chen, J. (2019) · Chemical Biology & Drug Design · doi:10.1111/cbdd.13623 · Cited by 12
Homology modeling and molecular dynamics study of chorismate synthase from Shigella flexneri
Zhou, H., Singh, N. J., & Kim, K. S. (2006) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2006.02.013 · Cited by 13
Mena‐Ulecia, K., & MacLeod‐Carey, D. (2018) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2018.04.004 · Cited by 13
Computation of Drug‐Binding Thermodynamics
Ferenczy, G. G. (2015) · Methods and principles in medicinal chemistry · doi:10.1002/9783527673025.ch3 · Cited by 13
Liu, X., Zheng, L., Cong, Y., Gong, Z., Yin, Z., Zhang, J. Z. H., Liu, Z., & Sun, Z. (2022) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-022-00487-w · Cited by 12
DNA damage-induced YTHDC1 O-GlcNAcylation promotes homologous recombination by enhancing m6A binding
Li, M., Li, J., Wang, Y., Zhao, J., Yuan, A., Dong, W., Kong, L., Dong, S., Qin, W., Yang, Y., et al. (2023) · Fundamental Research · doi:10.1016/j.fmre.2023.04.017 · Cited by 12
Alturki, M. S. (2024) · Marine Drugs · doi:10.3390/md22100455 · Cited by 12
Chantraine, C., Gomes, P. D. S. F. C., Mathelié‐Guinlet, M., Gomes, D. E. B., Zheng, Z., Clowry, J., Turley, M. B., Irvine, A. D., Geoghegan, J. A., Bernardi, R. C., et al. (2025) · Science Advances · doi:10.1126/sciadv.adu7457 · Cited by 12
Yu, Z.-H., Wen, X., & Xi, Z. (2010) · Science China Chemistry · doi:10.1007/s11426-010-0024-0 · Cited by 12
Farrokhzadeh, A., Akher, F. B., & Soliman, M. E. S. (2018) · Applied Biochemistry and Biotechnology · doi:10.1007/s12010-018-2914-0 · Cited by 13
Dissociation mechanism of GDP from Cdc42 via DOCK9 revealed by molecular dynamics simulations
Kang, N., Liu, J., & Zhao, Y. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25665 · Cited by 11
Salifu, E. Y., Agoni, C., Olotu, F. A., Dokurugu, Y. M., & Soliman, M. E. S. (2019) · Journal of Cellular Biochemistry · doi:10.1002/jcb.28891 · Cited by 13
Lin, B., Zhang, H., & Zheng, Q. (2020) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp00763c · Cited by 12
Mothay, D., & Ramesh, K. V. (2020) · Biologia · doi:10.2478/s11756-020-00590-z · Cited by 12
Click-designed vanilloid-triazole conjugates as dual inhibitors of AChE and Aβ aggregation
Elsbaey, M., Igarashi, Y., Ibrahim, M. A. A., & Elattar, E. M. (2023) · RSC Advances · doi:10.1039/d2ra07539c · Cited by 13
Murali, P., & Karuppasamy, R. (2023) · Anti-Cancer Agents in Medicinal Chemistry · doi:10.2174/1871520623666230125090815 · Cited by 12
Ibrahim, M. A. A., Abdeljawaad, K. A. A., Jaragh-Alhadad, L. A., Oraby, H. F., Atia, M. A. M., Alzahrani, O. R., Mekhemer, G. A. H., Moustafa, M., Shawky, A. M., Sidhom, P. A., et al. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2176360 · Cited by 12
Zhang, J., Cong, Y., Duan, L., & Zhang, J. Z. H. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00813 · Cited by 12
Singam, E. R. A., Balamurugan, K., Gopalakrishnan, R., Subramanian, S. R., Subramanian, V., & Ramasami, T. (2012) · Biopolymers · doi:10.1002/bip.22085 · Cited by 12
Sa, R., Fang, L., Huang, M., Li, Q., Wei, Y., & Wu, K. (2014) · The Journal of Physical Chemistry A · doi:10.1021/jp5064319 · Cited by 12
Designing Ligands to Bind Tightly to Proteins
Whitesides, G. M., Snyder, P. W., Moustakas, D. T., & Mirica, K. A. (2008) · IMPERIAL COLLEGE PRESS eBooks · doi:10.1142/9781848162013_0009 · Cited by 12
Li, D., Cai, Y., Teng, D., Li, W., Tang, Y., & Liu, G. (2019) · Chemical Biology & Drug Design · doi:10.1111/cbdd.13506 · Cited by 12
Current methods and applications in computational protein design for food industry
Chen, Q., Xiao, Y., Zhang, W., & Mu, W. (2019) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2019.1682513 · Cited by 12
Teng, D., Chen, J., Li, D., Wu, Z., Li, W., Tang, Y., & Liu, G. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00030 · Cited by 12
Transferability of conformational dependent charges from protein simulations
Genheden, S., Söderhjelm, P., & Ryde, U. (2011) · International Journal of Quantum Chemistry · doi:10.1002/qua.22967 · Cited by 12
Aki, E., Ertan‐Bolelli, T., Taşkın‐Tok, T., Öztürk, Ö., Ataei, S., Özen, Ç., Yıldız, İ., & Yalçın, İ. (2014) · SAR and QSAR in environmental research · doi:10.1080/1062936x.2014.923039 · Cited by 12
Sattarinezhad, E., Bordbar, A., & Fani, N. (2016) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2016.1196152 · Cited by 12
The equivalent potential of water molecules for electronic structure of cysteine
Wang, X.-M., Zheng, H.-P., & Li, C.-J. (2006) · The European Physical Journal B · doi:10.1140/epjb/e2006-00284-8 · Cited by 12
Incorporating receptor flexibility in the molecular design of protein interfaces
Li, L., Liang, S., Pilcher, M. M., & Meroueh, S. O. (2009) · Protein Engineering Design and Selection · doi:10.1093/protein/gzp042 · Cited by 12
Asada, T., Gouda, H., & Kollman, P. A. (2002) · Journal of the American Chemical Society · doi:10.1021/ja020774a · Cited by 12
Self-citationConformationally Restricted σ1 Receptor Antagonists from (−)-Isopulegol
Blicker, L., González‐Cano, R., Laurini, E., Nieto, F. R., Schmidt, J., Schepmann, D., Pricl, S., & Wünsch, B. (2023) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.2c02081 · Cited by 11
Purohit, P., Barik, D., Agasti, S., Panda, M., & Meher, B. R. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2212798 · Cited by 11
Hadni, H., Fitri, A., Benjelloun, A. T., Benzakour, M., Mcharfi, M., & Benbrahim, M. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2245051 · Cited by 12
Ramharack, P., Salifu, E. Y., & Agoni, C. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241814021 · Cited by 11
Shaaban, M. M., Teleb, M., Ragab, H. M., Singh, M., Elwakil, B. H., Heikal, L., Sriram, D., & Mahran, M. A. (2024) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2024.107179 · Cited by 11
HDBind: encoding of molecular structure with hyperdimensional binary representations
Jones, D., Zhang, X., Bennion, B. J., Pinge, S., Xu, W., Kang, J., Khaleghi, B., Moshiri, N., Allen, J., & Rosing, T. (2024) · Scientific Reports · doi:10.1038/s41598-024-80009-w · Cited by 12
Chen, Q., Yu, L., & Han, X. (2025) · Langmuir · doi:10.1021/acs.langmuir.4c05037 · Cited by 11
Modular Solid‐Phase Synthesis of Teroxazoles as a Class of α‐Helix Mimetics
Gomes, C. P., Metz, A., Bats, J. W., Gohlke, H., & Göbel, M. (2012) · European Journal of Organic Chemistry · doi:10.1002/ejoc.201200339 · Cited by 11
Computer aided design of FtsZ targeting oligopeptides
Pieraccini, S., Rendine, S., Jobichen, C., Domadia, P. N., Sivaraman, J., Francescato, P., Speranza, G., & Sironi, M. (2012) · RSC Advances · doi:10.1039/c2ra21886k · Cited by 11
Vinblastine perturbation of tubulin protofilament structure: a computational insight
Rendine, S., Pieraccini, S., & Sironi, M. (2010) · Physical Chemistry Chemical Physics · doi:10.1039/c0cp00594k · Cited by 11
Arif, A., Hashmi, M. A., Salam, S., Younus, H., & Mahmood, R. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2109756 · Cited by 11
Ibrahim, M. A. A., Ali, S. S. M., Abdeljawaad, K. A., Abdelrahman, A. H. M., Gabr, G., Shawky, A., Mekhemer, G., Sidhom, P. A., Paré, P., & Hegazy, M. (2023) · Journal of Taibah University for Science · doi:10.1080/16583655.2023.2182623 · Cited by 11
Ibrahim, M. A. A., Abdeljawaad, K. A. A., Abdelrahman, A. H. M., Sidhom, P. A., Tawfeek, A. M., Mekhemer, G. A. H., El‐Rahman, M. K. A., Dabbish, E., & Shoeib, T. (2023) · Pharmaceuticals · doi:10.3390/ph16071019 · Cited by 11
Alabbas, A. B. (2023) · Saudi Pharmaceutical Journal · doi:10.1016/j.jsps.2023.101745 · Cited by 11
Li, D., Han, J., Chen, H., Liang, L., Zhao, R., Liu, G., & Duan, Y. (2011) · Journal of Molecular Modeling · doi:10.1007/s00894-011-1205-2 · Cited by 11
Płazińska, A., Płaziński, W., & Jóźwiak, K. (2014) · Journal of Computational Chemistry · doi:10.1002/jcc.23563 · Cited by 11
Tonelli, M., Sparatore, A., Basilico, N., Cavicchini, L., Parapini, S., Tasso, B., Laurini, E., Pricl, S., Boido, V., & Sparatore, F. (2020) · Pharmaceuticals · doi:10.3390/ph13110339 · Cited by 11
Protein kinase C isozymes and their selectivity towards ruboxistaurin
Tang, S., Xiao, V., Wei, L., Whiteside, C. I., & Kotra, L. P. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21942 · Cited by 11
Tan, V. B. C., Zhang, B., Lim, K. M., & Tay, T. E. (2009) · Journal of Molecular Modeling · doi:10.1007/s00894-009-0514-1 · Cited by 11
Docking and Scoring in Drug Discovery
Spyrakis, F., Cozzini, P., & Kellogg, G. E. (2010) · Wiley eBooks · doi:10.1002/0471266949.bmc140 · Cited by 12
Gul, H., Assad, N., Nasreen, Z., Ahmad, N., Assad, Y., Khan, M. N., Vandy, A., Lahai, M., Hassan, M. N. U., & Ercişli, S. (2026) · PLoS ONE · doi:10.1371/journal.pone.0343273 · Cited by 10
Ibrahim, M. A. A., Abdeljawaad, K. A. A., Abdelrahman, A. H. M., Abdelhamid, M. M. H., Naeem, M. A., Mekhemer, G. A. H., Sidhom, P. A., Sayed, S. R. M., Paré, P. W., & Hegazy, M. F. (2023) · PLoS ONE · doi:10.1371/journal.pone.0288919 · Cited by 10
Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host–Guest Systems
Liu, X., Zheng, L., Qin, C., Li, Y., Zhang, J. Z. H., & Sun, Z. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01356 · Cited by 10
Ibrahim, M. A. A., Mahmoud, D. G. M., Abdelrahman, A. H. M., Abdeljawaad, K. A. A., Mekhemer, G. A. H., Shoeib, T., El‐Tayeb, M. A., Sidhom, P. A., Paré, P. W., & Hegazy, M. F. (2024) · PLoS ONE · doi:10.1371/journal.pone.0314422 · Cited by 10
Onisuru, O. O., & Achilonu, I. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.140526 · Cited by 10
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
Cluster analysis on conformational changes of the GDP/KRAS complex induced by A59G and D33E
Zhao, J., Wang, L., Bao, H., & Chen, J. (2021) · Chemical Physics Letters · doi:10.1016/j.cplett.2021.138995 · Cited by 10
Xia, W., He, L., Bao, J., Qi, Y., & Zhang, J. Z. H. (2021) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2021.1971558 · Cited by 10
Salifu, E. Y., Rashid, I. A., Issahaku, A. R., Osei, F., & Ayariga, J. A. (2023) · Frontiers in Drug Discovery · doi:10.3389/fddsv.2023.1087008 · Cited by 12
Ibrahim, M. A. A., Abdelhamid, M. M. H., Abdeljawaad, K. A. A., Abdelrahman, A. H. M., Mekhemer, G. A. H., Sidhom, P. A., Sayed, S. R. M., Paré, P. W., Hegazy, M. F., & Shoeib, T. (2023) · Molecules · doi:10.3390/molecules28155713 · Cited by 10
Molecular Interactions and Residues Involved in Force Generation in the T4 Viral DNA Packaging Motor
Migliori, A. D., Smith, D. E., & Arya, G. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.09.023 · Cited by 10
Silva, P. J., & Bernardo, C. E. P. (2014) · PeerJ · doi:10.7717/peerj.470 · Cited by 10
Moonsamy, S., Bhakat, S., Walker, R. C., & Soliman, M. E. S. (2015) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-015-0709-2 · Cited by 10
Appiah‐Kubi, P., & Soliman, M. E. S. (2016) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-016-0772-3 · Cited by 10
Computational Docking as a Tool for the Rational Design of Carbohydrate-Based Drugs
Frank, M. (2014) · Topics in medicinal chemistry · doi:10.1007/7355_2014_42 · Cited by 10
Packing interface energetics in different crystal forms of the λ Cro dimer
Ahlstrom, L. S., & Miyashita, O. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24478 · Cited by 11
Zhang, N., & Zhong, R. (2009) · Journal of Molecular Modeling · doi:10.1007/s00894-009-0582-2 · Cited by 10
Zhang, B., Su, Z., Tay, T. E., & Tan, V. B. C. (2009) · Journal of Molecular Modeling · doi:10.1007/s00894-009-0629-4 · Cited by 10
Discovery of novel bacterial elongation condensing enzyme inhibitors by virtual screening
Zheng, Z. S., Parsons, J. B., Tangallapally, R. P., Zhang, W., Rock, C. O., & Lee, R. E., Jr. (2014) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2014.03.033 · Cited by 10
Appiah‐Kubi, P., & Soliman, M. E. S. (2015) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2015.1117991 · Cited by 10
The impact of surface area, volume, curvature, and Lennard–Jones potential to solvation modeling
Nguyen, D. D., & Wei, G. (2016) · Journal of Computational Chemistry · doi:10.1002/jcc.24512 · Cited by 10
The equivalent potential of water molecules for electronic structure of lysine
Li, C., Zheng, H., & Wang, X. (2007) · Science in China. Series G, Physics, mechanics & astronomy/Science in China. Series G, Physics, Mechanics & Astronomy · doi:10.1007/s11433-007-0003-4 · Cited by 10
The equivalent potential of water molecules for the electronic structure of histidine
Li, C., Zheng, H., & Wang, X. (2007) · Journal of Physics Condensed Matter · doi:10.1088/0953-8984/19/11/116102 · Cited by 10
Munei, Y., Hengphasatporn, K., Hori, Y., Harada, R., & Shigeta, Y. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c01253 · Cited by 9
RoseTTAFold diffusion-guided short peptide design: a case study of binders against Keap1/Nrf2
Morena, F., Cencini, C., Emiliani, C., & Martino, S. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.02.032 · Cited by 12
Hasan, M. N., Sharma, S., Mallen, J. J., & Saha, A. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c04085 · Cited by 10
Li, P., Tan, J., Liu, M., Zhang, X. Y., Chen, W. Z., & Wang, C. X. (2011) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2011.10507387 · Cited by 9
Metadata
- Authors
- Massova, I., & Kollman, P. A.
- Affiliations
- University of California, San Francisco (US)
- Venue
- Perspectives in Drug Discovery and Design
- Published
- 2000-06
- Volume
- 18
- Issue
- 1
- Pages
- 113-135
- ISSN
- 0928-2866 (ISSN-L)
- 1573-9023
- OpenAlex
- W1549357029
- Cited by
- 1,015
- References
- 55
- Citations by year
- 2026: 58 · 2025: 85 · 2024: 64 · 2023: 85 · 2022: 67 · 2021: 83 · 2020: 57 · 2019: 46 · 2018: 48 · 2017: 47 · 2016: 46 · 2015: 39 · 2014: 45 · 2013: 36 · 2012: 34
- FWCI
- 10.76
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Perspectives in Drug Discovery and Design (publishedVersion)
- Funders
- National Institute for Health and Care Research
- National Institutes of Health
- Topics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- MM-PBSA, ligand binding prediction, binding free energy, solvent effects, solvation energy, scanning mutagenesis, molecular dynamics, high-throughput screening, binding affinity ranking
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review