The DOI matches its Crossref record; 80 of the 81 references it cites were found in a registry or an index.
Multiple diverse ligands binding at a single protein site: A matter of pre‐existing populations
Open accessAbstract
Here, we comment on the steadily increasing body of data showing that proteins with specificity actually bind ligands of diverse shapes, sizes, and composition. Such a phenomenon is not surprising when one considers that binding is a dynamic process with populations in equilibrium and that the shape of the binding site is strongly influenced by the molecular partner. It derives implicitly from the concept of populations. All proteins, specific and nonspecific, exist in ensembles of substates. If the library of ligands in solution is large enough, favorably matching ligands with altered shapes and sizes can be expected to bind, with a redistribution of the protein populations. Point mutations at spatially distant sites may exert large conformational rearrangements and hinge effects, consistent with mutations away from the binding site leading to population shifts and (cross‐)drug resistance. A similar effect is observed in protein superfamilies, in which different sequences with similar topologies display similar large‐scale dynamic motions. The hinges are frequently at analogous sites, yet with different substrate specificity. Similar topologies yield similar conformational isomers, although with different distributions of population times, owing to the change in the conditions, that is, the change in the sequences. In turn, different distributions relate to binding of different sizes and shapes. Hence, the binding site shape and size are defined by the ligand. They are not independent entities of fixed proportions and cannot be analyzed independently of the binding partner. Such a proposition derives from viewing proteins as dynamic distributions, presenting to the incoming ligands a range of binding site shapes. It illustrates how presumably specific binding molecules can bind multiple ligands. In terms of drug design, the ability of a single receptor to recognize many dissimilar ligands shows the need to consider more diverse molecules. It provides a rationale for higher affinity inhibitors that are not derived from substrates at their transition states and indicates flexible docking schemes.
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
“These can potentially favorably interact with ensembles of ligands of variable sizes.219,225”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [219]
In the citing paper
“Hinge sites with multiple conformations are often the binding sites for multiple-ligands,219”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [219]
In the citing paper
“Depending on the distributions of the conformers and their conformational variability, they provide a gradient of binding site conformations of different shapes and volumes.”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [219]
In the citing paper
“Protein dynamics have been shown to be universally important for protein-ligand interaction.219”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [219]
Citations
Cites
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
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574
Murzin, A. G., Brenner, S. E., Hubbard, T., & Chothia, C. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80134-2 · Cited by 6,435
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
Wright, P. E., & Dyson, H. J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3110 · Cited by 2,968
Proteins: Structures and Molecular Properties
Creighton, T. E. (1986) · Medical Entomology and Zoology · Cited by 2,645
Application of a Theory of Enzyme Specificity to Protein Synthesis.
Koshland, D. (1958) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.44.2.98 · Cited by 2,140
Why are ?natively unfolded? proteins unstructured under physiologic conditions?
Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20001115)41:3 · Cited by 2,097
Anatomy of hot spots in protein interfaces
Bogan, A. A., & Thorn, K. S. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1843 · Cited by 1,988
A Hot Spot of Binding Energy in a Hormone-Receptor Interface
Clackson, T., & Wells, J. A. (1995) · Science · doi:10.1126/science.7529940 · Cited by 1,987
Principles of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
Self-citation
Flagged first, then by citations
1 of the 81 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Items 101–200 of 424
Bhardwaj, V. K., & Purohit, R. (2019) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2019.1621210 · Cited by 78
Wani, T. A., Bakheit, A. H. H., Al‐Majed, A. A., Altwaijry, N. A., Baquaysh, A., Aljuraisy, A., & Zargar, S. (2021) · Journal of Molecular Liquids · doi:10.1016/j.molliq.2021.115934 · Cited by 77
Gu, S., Silva, D., Meng, L., Yue, A., & Huang, X. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003767 · Cited by 71
Londhe, A. M., Gadhe, C. G., Lim, S. M., & Pae, A. N. (2019) · Molecules · doi:10.3390/molecules24224085 · Cited by 72
Kurakin, A. V. (2010) · Theoretical Biology and Medical Modelling · doi:10.1186/1742-4682-7-12 · Cited by 74
Spérandio, O., Mouawad, L., Pinto, E., Villoutreix, B. O., Pérahia, D., & Miteva, M. A. (2010) · European Biophysics Journal · doi:10.1007/s00249-010-0592-0 · Cited by 76
Spyrakis, F., Benedetti, P., Decherchi, S., Rocchia, W., Cavalli, A., Alcaro, S., Ortuso, F., Baroni, M., & Cruciani, G. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00169 · Cited by 71
Mechanisms of recognition of amyloid-β (Aβ) monomer, oligomer, and fibril by homologous antibodies
Zhao, J., Nussinov, R., & Ma, B. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.801514 · Cited by 71
Self-citationSmall-Molecule Inhibitors of IL-2/IL-2R: Lessons Learned and Applied
Wilson, C. G. M., & Arkin, M. R. (2010) · Current topics in microbiology and immunology · doi:10.1007/82_2010_93 · Cited by 74
Wani, T. A., Alsaif, N. A., Alanazi, M. M., Bakheit, A. H. H., Khan, A. A., & Zargar, S. (2021) · Journal of Molecular Liquids · doi:10.1016/j.molliq.2021.117542 · Cited by 67
Antidiabetic and antimalarial biguanide drugs are metal-interactive antiproteolytic agents
Sweeney, D., Raymer, M. L., & Lockwood, T. D. (2003) · Biochemical Pharmacology · doi:10.1016/s0006-2952(03)00338-1 · Cited by 66
Multi-Conformer Ensemble Docking to Difficult Protein Targets
Ellingson, S. R., Miao, Y., Baudry, J. Y., & Smith, J. C. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp506511p · Cited by 68
Lu, Z.-L., Gallagher, R., Sellar, R., Coetsee, M., & Millar, R. P. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m413520200 · Cited by 67
Wang, C., Karpowich, N. K., Hunt, J. F., Rance, M., & Palmer, A. G. I. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.07.001 · Cited by 67
Idili, A., Plaxco, K. W., Vallée‐Bélisle, A., & Ricci, F. (2013) · ACS Nano · doi:10.1021/nn404305e · Cited by 66
Boys, B. L., & Konermann, L. (2006) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2006.08.013 · Cited by 65
Receptor-ligand interactions for optimized endocytosis in targeted therapies
Sung, Y., Choi, Y., Kim, E. S., Ryu, J. H., & Kwon, I. C. (2025) · Journal of Controlled Release · doi:10.1016/j.jconrel.2025.01.060 · Cited by 64
A new insight into protein-protein interactions and the effect of conformational alterations in PCNA
Bhardwaj, V. K., & Purohit, R. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.01.212 · Cited by 65
Structured Crowding and Its Effects on Enzyme Catalysis
Ma, B., & Nussinov, R. (2013) · Topics in current chemistry · doi:10.1007/128_2012_316 · Cited by 62
Self-citationEffective handling of induced‐fit motion in flexible docking
Mizutani, M., Takamatsu, Y., Ichinose, T., Nakamura, K., & Itai, A. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20931 · Cited by 63
SiteLight: Binding‐site prediction using phage display libraries
Halperin, I., Wolfson, H. J., & Nussinov, R. (2003) · Protein Science · doi:10.1110/ps.0237103 · Cited by 64
Self-citationLópez, C. J., Oga, S., & Hubbell, W. L. (2012) · Biochemistry · doi:10.1021/bi3005686 · Cited by 62
The principle of conformational signaling
Tompa, P. (2016) · Chemical Society Reviews · doi:10.1039/c6cs00011h · Cited by 63
Prasad, J. C., Goldstone, J. V., Camacho, C. J., Vajda, S., & Stegeman, J. J. (2007) · Biochemistry · doi:10.1021/bi062320m · Cited by 59
Ji, H., De, K., Shen, L., Chen, L., Ma, B., & Zhang, H. (2007) · Genome biology · doi:10.1186/gb-2007-8-8-r176 · Cited by 61
Self-citationLessons in Organic Fluorescent Probe Discovery
Wagh, S. B., Maslivetc, V. A., Clair, J. J. L., & Kornienko, A. (2021) · ChemBioChem · doi:10.1002/cbic.202100171 · Cited by 58
Chan, A. H., Wereszczynski, J., Amer, B. R., Yi, S. W., Jung, M. E., McCammon, J. A., & Clubb, R. (2013) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12167 · Cited by 60
Scale-free flow of life: on the biology, economics, and physics of the cell
Kurakin, A. V. (2009) · Theoretical Biology and Medical Modelling · doi:10.1186/1742-4682-6-6 · Cited by 58
Kua, J., Zhang, Y., Eslami, A. C., Butler, J. R., & McCammon, J. A. (2003) · Protein Science · doi:10.1110/ps.03318603 · Cited by 57
Kotzsch, A., Nickel, J., Seher, A., Heinecke, K., van Geersdaele, L., Herrmann, T., Sebald, W., & Mueller, T. D. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m706029200 · Cited by 56
Guiraudie-Capraz, G. (2003) · Chemical Senses · doi:10.1093/chemse/bjg052 · Cited by 56
“Molecular Chameleons”. Design and Synthesis of a Second Series of Flexible Nucleosides
Seley‐Radtke, K. L., Salim, S., Zhang, L., & O’Daniel, P. I. (2005) · The Journal of Organic Chemistry · doi:10.1021/jo048218h · Cited by 56
Liu, J., & Nussinov, R. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000527 · Cited by 55
Self-citationDurrant, J. D., Friedman, A. J., Rogers, K. E., & McCammon, J. A. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400042y · Cited by 55
Targeting G protein coupled receptor-related pathways as emerging molecular therapies
Ghanemi, A. (2015) · Saudi Pharmaceutical Journal · doi:10.1016/j.jsps.2013.07.007 · Cited by 53
Comparative Modeling: The State of the Art and Protein Drug Target Structure Prediction
Liu, T., Tang, G. W., & Capriotti, E. (2011) · Combinatorial Chemistry & High Throughput Screening · doi:10.2174/138620711795767811 · Cited by 56
Lerch, M. T., Horwitz, J., McCoy, J., & Hubbell, W. L. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320124110 · Cited by 53
Molecular Recognition in the Case of Flexible Targets
Ivetac, A., & McCammon, J. A. (2011) · Current Pharmaceutical Design · doi:10.2174/138161211796355056 · Cited by 53
Promiscuous and specific recognition among ephrins and Eph receptors
Dai, D., Huang, Q., Nussinov, R., & Ma, B. (2014) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2014.07.002 · Cited by 51
Self-citationChoudhury, C., Priyakumar, U. D., & Sastry, G. N. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/ci500737b · Cited by 51
Perricone, U., Gulotta, M. R., Lombino, J., Parrino, B., Cascioferro, S., Diana, P., Cirrincione, G., & Padova, A. (2018) · MedChemComm · doi:10.1039/c8md00166a · Cited by 54
Limitations to the structure‐based design of HIV‐1 vaccine immunogens
Regenmortel, M. H. V. V. (2011) · Journal of Molecular Recognition · doi:10.1002/jmr.1116 · Cited by 50
The spatial structure of cell signaling systems
Nussinov, R. (2013) · Physical Biology · doi:10.1088/1478-3975/10/4/045004 · Cited by 49
Self-citationInduced fit or conformational selection for RNA/U1A folding
Fang, Q., Chen, Y., Wu, M., Li, Y., Zhang, J., & Chen, H. (2010) · RNA · doi:10.1261/rna.2008110 · Cited by 48
Lapelosa, M., Gallicchio, E., Arnold, G. F., Arnold, E., & Levy, R. M. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.10.089 · Cited by 48
Salinthone, S., Schillace, R. V., Marracci, G., BOURDETTE, D. N., & Carr, D. W. (2008) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2008.05.003 · Cited by 48
Exploiting Conformational Ensembles in Modeling Protein–Protein Interactions on the Proteome Scale
Kuzu, G., Gursoy, A., Nussinov, R., & Keskin, O. (2013) · Journal of Proteome Research · doi:10.1021/pr400006k · Cited by 47
Self-citationIn Silico Elucidation of the Recognition Dynamics of Ubiquitin
Long, D., & Brüschweiler, R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002035 · Cited by 49
Hierarchical and multi-resolution representation of protein flexibility
Zhao, Y., Stoffler, D., & Sanner, M. F. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl481 · Cited by 45
Molecular Dynamics Simulation of Phosphorylated KID Post-Translational Modification
Chen, H. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006516 · Cited by 46
Tsai, C., & Nussinov, R. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c3cp54253j · Cited by 47
Self-citationLampe, J. N., Brandman, R., Sivaramakrishnan, S., & de Montellano, P. R. O. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.087593 · Cited by 45
Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development
Duran‐Frigola, M., Mosca, R., & Aloy, P. (2013) · Chemistry & Biology · doi:10.1016/j.chembiol.2013.03.004 · Cited by 44
Pre‐Training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding
Wu, F., Jin, S., Jiang, Y., Jin, X., Tang, B., Niu, Z., Liu, X., Zhang, Q., Zeng, X., & Li, S. Z. (2022) · Advanced Science · doi:10.1002/advs.202203796 · Cited by 46
Asthana, S., Shukla, S., Vargiu, A. V., Ceccarelli, M., Ruggerone, P., Paglietti, G., Marongiu, M. E., Blois, S., Giliberti, G., & Colla, P. L. (2013) · Biochemistry · doi:10.1021/bi400107h · Cited by 42
Wang, W., Ye, W., Yu, Q., Jiang, C., Zhang, J., Luo, R., & Chen, H. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp4010967 · Cited by 41
Akten, E. D., Cansu, S., & Doruker, P. (2009) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2009.10507292 · Cited by 42
Gentili, P. L. (2024) · Biomimetics · doi:10.3390/biomimetics9020121 · Cited by 42
Structural, Energetic, and Dynamic Aspects of Ligand–Receptor Interactions
Motiejunas, D., & Wade, R. C. (2007) · Elsevier eBooks · doi:10.1016/b0-08-045044-x/00250-9 · Cited by 41
Unarta, I. C., Cao, S., Kubo, S., Wang, W., Cheung, P. P., Gao, X., Takada, S., & Huang, X. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2024324118 · Cited by 39
AID‐Initiated Purposeful Mutations in Immunoglobulin Genes
Goodman, M. F., Scharff, M. D., & Romesberg, F. E. (2007) · Advances in immunology · doi:10.1016/s0065-2776(06)94005-x · Cited by 41
Pletneva, E. V., Sundd, M., Fulton, D. B., & Andreotti, A. H. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.12.073 · Cited by 41
Target Based Drug Design - A Reality in Virtual Sphere
Verma, S. K., & Prabhakar, Y. S. (2015) · Current Medicinal Chemistry · doi:10.2174/0929867322666150209151209 · Cited by 43
Prediction of Interacting Single-Stranded RNA Bases by Protein-Binding Patterns
Shulman‐Peleg, A., Shatsky, M., Nussinov, R., & Wolfson, H. J. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.03.043 · Cited by 40
Self-citationRecent Progress in Antibody Epitope Prediction
Zeng, X., Bai, G., Sun, C., & Ma, B. (2023) · Antibodies · doi:10.3390/antib12030052 · Cited by 44
Self-citationIn Silico Assessment of Potential Druggable Pockets on the Surface of α1-Antitrypsin Conformers
Patschull, A. O. M., Gooptu, B., Ashford, P., Daviter, T., & Nobeli, I. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036612 · Cited by 41
Durrant, J. D., Bush, R. M., & Amaro, R. E. (2016) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b02655 · Cited by 42
Juritz, E., Fornasari, M. S., Martelli, P. L., Fariselli, P., Casadio, R., & Parisi, G. D. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-s4-s5 · Cited by 38
Reengineering the pharmaceutical industry by crash-testing molecules
Swaan, P. W., & Ekins, S. (2005) · Drug Discovery Today · doi:10.1016/s1359-6446(05)03557-9 · Cited by 38
Inhibitor Specificity via Protein Dynamics
Ferrari, S., Costi, P. M., & Wade, R. C. (2003) · Chemistry & Biology · doi:10.1016/j.chembiol.2003.11.012 · Cited by 38
Dynamic multiprotein assemblies shape the spatial structure of cell signaling
Nussinov, R., & Jang, H. (2014) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2014.07.002 · Cited by 38
Self-citationSynthetic Peptide Vaccines and the Search for Neutralization B Cell Epitopes
Regenmortel, M. H. V. V. (2019) · Springer eBooks · doi:10.1007/978-3-030-32459-9_3 · Cited by 37
The Synthesis of Azapeptidomimetic β-Lactam Molecules as Potential Protease Inhibitors
Malachowski, W. P., Tie, C., Wang, K., & Broadrup, R. L. (2002) · The Journal of Organic Chemistry · doi:10.1021/jo026280d · Cited by 37
Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
Xie, Z., & Hwang, M. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts182 · Cited by 36
Ligand binding and allostery can emerge simultaneously
Liang, J., Kim, J. R., Boock, J. T., Mansell, T. J., & Ostermeier, M. (2007) · Protein Science · doi:10.1110/ps.062706007 · Cited by 36
Engineering an Allosteric Control of Protein Function
Vishweshwaraiah, Y. L., Chen, J., & Dokholyan, N. V. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c11640 · Cited by 33
Collective Dynamics Differentiates Functional Divergence in Protein Evolution
Glembo, T. J., Farrell, D. W., Gerek, Z. N., Thorpe, M. F., & Ozkan, S. B. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002428 · Cited by 34
Gene-specific transcription activation via long-range allosteric shape-shifting
Tsai, C., & Nussinov, R. (2011) · Biochemical Journal · doi:10.1042/bj20110972 · Cited by 35
Self-citationThe origin and extent of coarse‐grained regularities in protein internal packing
Bagci, E. Z., Kloczkowski, A., Jernigan, R. L., & Bahar, İ. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10435 · Cited by 34
Molecular determinants of protein evolvability
Buda, K., Miton, C. M., Fan, X. C., & Tokuriki, N. (2023) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2023.05.009 · Cited by 32
Bijari, N., Ghobadi, S., Mahdiuni, H., Khodarahmi, R., & Ghadami, S. A. (2015) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2015.06.028 · Cited by 34
Verkhivker, G. M., Bouzida, D., Gehlhaar, D. K., Rejto, P. A., Freer, S. T., & Rose, P. W. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10164 · Cited by 34
Engineering and design of ligand-induced conformational change in proteins
Mizoue, L. S., & Chazin, W. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00348-2 · Cited by 33
Protein Hot Spots: The Islands of Stability
Kuttner, Y. Y., & Engel, S. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.11.009 · Cited by 32
Higo, J., Dasgupta, B., Mashimo, T., Kasahara, K., Fukunishi, Y., & Nakamura, H. (2015) · Journal of Computational Chemistry · doi:10.1002/jcc.23948 · Cited by 32
Protein Conformational Diversity Modulates Sequence Divergence
Juritz, E., Palópoli, N., Fornasari, M. S., Fernández-Alberti, S., & Parisi, G. D. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss080 · Cited by 34
Salinthone, S., Schillace, R. V., Tsang, C., Regan, J. W., BOURDETTE, D. N., & Carr, D. W. (2010) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2010.05.008 · Cited by 32
Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations
Shulman‐Peleg, A., Mintz, S., Nussinov, R., & Wolfson, H. J. (2004) · Lecture notes in computer science · doi:10.1007/978-3-540-30219-3_17 · Cited by 32
Self-citationRepositioned Drugs for Chagas Disease Unveiled via Structure-Based Drug Repositioning
Adasme, M. F., Bolz, S. N., Adelmann, L., Salentin, S., Haupt, V. J., Rodríguez, A. M., Nogueda‐Torres, B., Castillo-Campos, V., Yépez‐Mulia, L., Fuentes-Vicente, J. A. D., et al. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21228809 · Cited by 31
Selvam, P., De, S., Paira, P., Kumar, S. K. A., Ramasamy, S. K., Moorthy, A., Ghosh, A., Kuo, Y., Banerjee, S., & Kumar, J. S. (2022) · Dalton Transactions · doi:10.1039/d2dt02237k · Cited by 31
Segmented Transition Pathway of the Signaling Protein Nitrogen Regulatory Protein C
Lei, M., Velos, J., Gardino, A. K., Kivenson, A., Karplus, M., & Kern, D. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.06.065 · Cited by 31
Conformational selection or induced fit for Brinker and DNA recognition
Fang, Q., Jiang, Y., Chen, Y., Wu, M., Yan, G., Ye, W., Li, Y., Zhang, J., & Chen, H. (2010) · Physical Chemistry Chemical Physics · doi:10.1039/c0cp00701c · Cited by 31
Database of ligand-induced domain movements in enzymes
Qi, G., & Hayward, S. (2009) · BMC Structural Biology · doi:10.1186/1472-6807-9-13 · Cited by 32
Adaptive Mutations Alter Antibody Structure and Dynamics during Affinity Maturation
Adhikary, R., Yu, W., Oda, M., Walker, R. C., Chen, T., Stanfield, R. L., Wilson, I. A., Zimmermann, J., & Romesberg, F. E. (2015) · Biochemistry · doi:10.1021/bi501417q · Cited by 31
Conformational diversity and computational enzyme design
Lassila, J. K. (2010) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2010.08.010 · Cited by 30
Perricone, U., Wieder, M., Seidel, T., Langer, T., Padova, A., Almerico, A. M., & Tutone, M. (2017) · ChemMedChem · doi:10.1002/cmdc.201600526 · Cited by 30
Ahmed, S., Sony, S. A., Chowdhury, M. B., Ullah, M. M., Paul, S., & Hossain, T. (2020) · Scientific Reports · doi:10.1038/s41598-020-76355-0 · Cited by 30
Mechanism of activation and the rewired network: New drug design concepts
Nussinov, R., Zhang, M., Maloney, R., Tsai, C., Yavuz, B. R., Tunçbağ, N., & Jang, H. (2021) · Medicinal Research Reviews · doi:10.1002/med.21863 · Cited by 30
Self-citationAdvances in fragment-based drug discovery platforms
Orita, M., Warizaya, M., Amano, Y., Ohno, K., & Niimi, T. (2009) · Expert Opinion on Drug Discovery · doi:10.1517/17460440903317580 · Cited by 32
Kurakin, A. V. (2007) · Journal of Molecular Recognition · doi:10.1002/jmr.839 · Cited by 29
Metadata
- Authors
- Ma, B., Shatsky, M., Wolfson, H. J., & Nussinov, R.
- Affiliations
- National Cancer Institute (US)
- Tel Aviv University (IL)
- Corresponding author
- Nussinov, Ruth
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2002-02
- Volume
- 11
- Issue
- 2
- Pages
- 184-197
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- PMC
- PMC2373439
- OpenAlex
- W2112053365
- Cited by
- 420
- References
- 81
- Citations by year
- 2026: 5 · 2025: 15 · 2024: 7 · 2023: 16 · 2022: 12 · 2021: 15 · 2020: 13 · 2019: 20 · 2018: 20 · 2017: 10 · 2016: 13 · 2015: 16 · 2014: 17 · 2013: 28 · 2012: 20
- FWCI
- 1.71
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Protein Science (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (n01co12400-79-0-22)
- National Cancer Institute (N01CO12400, N01-CO-012400)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Interaction Studies and Fluorescence Analysis
- Keywords
- ligand specificity, protein conformational ensembles, protein dynamics, ligand-induced conformational change, point mutations, protein superfamilies, conformational isomers, flexible docking, drug design
- MeSH terms
- Binding Sites, Ligands, Models, Molecular, Models, Theoretical, Protein Binding, Protein Conformation, Proteins, Combinatorial Chemistry Techniques
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
