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Number Cited by Other Article(s)
1
Yang Z, Zeng X, Zhao Y, Chen R. AlphaFold2 and its applications in the fields of biology and medicine. Signal Transduct Target Ther 2023;8:115. [PMID: 36918529 PMCID: PMC10011802 DOI: 10.1038/s41392-023-01381-z] [Citation(s) in RCA: 100] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/27/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023]  Open
2
Nagaraju M, Liu H. A scoring function for the prediction of protein complex interfaces based on the neighborhood preferences of amino acids. Acta Crystallogr D Struct Biol 2023;79:31-39. [PMID: 36601805 DOI: 10.1107/s2059798322011858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]  Open
3
Bongirwar V, Mokhade AS. Different methods, techniques and their limitations in protein structure prediction: A review. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022;173:72-82. [PMID: 35588858 DOI: 10.1016/j.pbiomolbio.2022.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 04/16/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022]
4
Machine learning/molecular dynamic protein structure prediction approach to investigate the protein conformational ensemble. Sci Rep 2022;12:10018. [PMID: 35705565 PMCID: PMC9200820 DOI: 10.1038/s41598-022-13714-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/11/2022] [Indexed: 11/25/2022]  Open
5
Peng CX, Zhou XG, Zhang GJ. De novo Protein Structure Prediction by Coupling Contact With Distance Profile. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:395-406. [PMID: 32750861 DOI: 10.1109/tcbb.2020.3000758] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
6
Xia YH, Peng CX, Zhou XG, Zhang GJ. A Sequential Niche Multimodal Conformational Sampling Algorithm for Protein Structure Prediction. Bioinformatics 2021;37:4357-4365. [PMID: 34245242 DOI: 10.1093/bioinformatics/btab500] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/23/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022]  Open
7
Kwon Y, Lee J. MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES. J Cheminform 2021;13:24. [PMID: 33736687 PMCID: PMC7977239 DOI: 10.1186/s13321-021-00501-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/27/2021] [Indexed: 12/22/2022]  Open
8
Zhang GJ, Wang XQ, Ma LF, Wang LJ, Hu J, Zhou XG. Two-Stage Distance Feature-based Optimization Algorithm for De novo Protein Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:2119-2130. [PMID: 31107659 DOI: 10.1109/tcbb.2019.2917452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
9
Chen X, Song S, Ji J, Tang Z, Todo Y. Incorporating a multiobjective knowledge-based energy function into differential evolution for protein structure prediction. Inf Sci (N Y) 2020. [DOI: 10.1016/j.ins.2020.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
10
Lee J, Brooks BR. Direct global optimization of Onsager-Machlup action using Action-CSA. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
11
Liu S, Xiang X, Gao X, Liu H. Neighborhood Preference of Amino Acids in Protein Structures and its Applications in Protein Structure Assessment. Sci Rep 2020;10:4371. [PMID: 32152349 PMCID: PMC7062742 DOI: 10.1038/s41598-020-61205-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 02/24/2020] [Indexed: 12/02/2022]  Open
12
Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling. PLoS Comput Biol 2019;15:e1007219. [PMID: 31846452 PMCID: PMC6938380 DOI: 10.1371/journal.pcbi.1007219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/31/2019] [Accepted: 11/13/2019] [Indexed: 01/02/2023]  Open
13
Li ZW, Sun K, Hao XH, Hu J, Ma LF, Zhou XG, Zhang GJ. Loop Enhanced Conformational Resampling Method for Protein Structure Prediction. IEEE Trans Nanobioscience 2019;18:567-577. [PMID: 31180866 DOI: 10.1109/tnb.2019.2922101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
14
Song S, Ji J, Chen X, Gao S, Tang Z, Todo Y. Adoption of an improved PSO to explore a compound multi-objective energy function in protein structure prediction. Appl Soft Comput 2018. [DOI: 10.1016/j.asoc.2018.07.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
15
Gao S, Song S, Cheng J, Todo Y, Zhou M. Incorporation of Solvent Effect into Multi-Objective Evolutionary Algorithm for Improved Protein Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:1365-1378. [PMID: 28534784 DOI: 10.1109/tcbb.2017.2705094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
16
AIMOES: Archive information assisted multi-objective evolutionary strategy for ab initio protein structure prediction. Knowl Based Syst 2018. [DOI: 10.1016/j.knosys.2018.01.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
17
Joo K, Heo S, Joung I, Hong SH, Lee SJ, Lee J. Data-assisted protein structure modeling by global optimization in CASP12. Proteins 2018;86 Suppl 1:240-246. [PMID: 29341255 DOI: 10.1002/prot.25457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 12/29/2017] [Accepted: 01/08/2018] [Indexed: 12/26/2022]
18
Hong SH, Joung I, Flores-Canales JC, Manavalan B, Cheng Q, Heo S, Kim JY, Lee SY, Nam M, Joo K, Lee IH, Lee SJ, Lee J. Protein structure modeling and refinement by global optimization in CASP12. Proteins 2017;86 Suppl 1:122-135. [PMID: 29159837 DOI: 10.1002/prot.25426] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022]
19
Zhang GJ, Zhou XG, Yu XF, Hao XH, Yu L. Enhancing Protein Conformational Space Sampling Using Distance Profile-Guided Differential Evolution. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017;14:1288-1301. [PMID: 28113726 DOI: 10.1109/tcbb.2016.2566617] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
20
Hao XH, Zhang GJ, Zhou XG. Conformational Space Sampling Method Using Multi-Subpopulation Differential Evolution for De novo Protein Structure Prediction. IEEE Trans Nanobioscience 2017;16:618-633. [DOI: 10.1109/tnb.2017.2749243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
21
Inverse Resolution Limit of Partition Density and Detecting Overlapping Communities by Link-Surprise. Sci Rep 2017;7:12399. [PMID: 28963540 PMCID: PMC5622083 DOI: 10.1038/s41598-017-12432-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/04/2017] [Indexed: 11/16/2022]  Open
22
Lee J, Lee IH, Joung I, Lee J, Brooks BR. Finding multiple reaction pathways via global optimization of action. Nat Commun 2017;8:15443. [PMID: 28548089 PMCID: PMC5458546 DOI: 10.1038/ncomms15443] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/24/2017] [Indexed: 12/25/2022]  Open
23
Heo S, Lee J, Joo K, Shin HC, Lee J. Protein Loop Structure Prediction Using Conformational Space Annealing. J Chem Inf Model 2017;57:1068-1078. [DOI: 10.1021/acs.jcim.6b00742] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
24
Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. J Comput Aided Mol Des 2016;31:71-85. [PMID: 27677749 DOI: 10.1007/s10822-016-9968-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/08/2016] [Indexed: 12/11/2022]
25
Lamiable A, Thevenet P, Tufféry P. A critical assessment of hidden markov model sub-optimal sampling strategies applied to the generation of peptide 3D models. J Comput Chem 2016;37:2006-16. [PMID: 27317417 DOI: 10.1002/jcc.24422] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/03/2016] [Accepted: 05/17/2016] [Indexed: 12/23/2022]
26
Kinch LN, Li W, Monastyrskyy B, Kryshtafovych A, Grishin NV. Evaluation of free modeling targets in CASP11 and ROLL. Proteins 2016;84 Suppl 1:51-66. [PMID: 26677002 DOI: 10.1002/prot.24973] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/12/2015] [Indexed: 12/25/2022]
27
Joo K, Joung I, Cheng Q, Lee SJ, Lee J. Contact-assisted protein structure modeling by global optimization in CASP11. Proteins 2016;84 Suppl 1:189-99. [DOI: 10.1002/prot.24975] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 11/24/2015] [Accepted: 12/12/2015] [Indexed: 11/09/2022]
28
Joung I, Lee SY, Cheng Q, Kim JY, Joo K, Lee SJ, Lee J. Template-free modeling by LEE and LEER in CASP11. Proteins 2015;84 Suppl 1:118-30. [DOI: 10.1002/prot.24944] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/26/2015] [Accepted: 10/11/2015] [Indexed: 12/25/2022]
29
Joo K, Joung I, Lee J, Lee J, Lee W, Brooks B, Lee SJ, Lee J. Protein structure determination by conformational space annealing using NMR geometric restraints. Proteins 2015;83:2251-62. [PMID: 26454251 DOI: 10.1002/prot.24941] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 09/19/2015] [Accepted: 09/22/2015] [Indexed: 11/06/2022]
30
Joo K, Joung I, Lee SY, Kim JY, Cheng Q, Manavalan B, Joung JY, Heo S, Lee J, Nam M, Lee IH, Lee SJ, Lee J. Template based protein structure modeling by global optimization in CASP11. Proteins 2015;84 Suppl 1:221-32. [PMID: 26329522 DOI: 10.1002/prot.24917] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/04/2015] [Accepted: 08/21/2015] [Indexed: 11/11/2022]
31
Vallat B, Madrid-Aliste C, Fiser A. Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures. PLoS Comput Biol 2015;11:e1004419. [PMID: 26252221 PMCID: PMC4529212 DOI: 10.1371/journal.pcbi.1004419] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/30/2015] [Indexed: 12/25/2022]  Open
32
Shen Y, Maupetit J, Derreumaux P, Tufféry P. Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction. J Chem Theory Comput 2014;10:4745-58. [DOI: 10.1021/ct500592m] [Citation(s) in RCA: 416] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
33
Lee J, Gross SP, Lee J. Improved network community structure improves function prediction. Sci Rep 2014;3:2197. [PMID: 23852097 PMCID: PMC3711050 DOI: 10.1038/srep02197] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 06/24/2013] [Indexed: 12/15/2022]  Open
34
Shen Y, Picord G, Guyon F, Tuffery P. Detecting protein candidate fragments using a structural alphabet profile comparison approach. PLoS One 2013;8:e80493. [PMID: 24303019 PMCID: PMC3841190 DOI: 10.1371/journal.pone.0080493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/03/2013] [Indexed: 01/28/2023]  Open
35
Joo K, Lee J, Sim S, Lee SY, Lee K, Heo S, Lee IH, Lee SJ, Lee J. Protein structure modeling for CASP10 by multiple layers of global optimization. Proteins 2013;82 Suppl 2:188-95. [PMID: 23966235 DOI: 10.1002/prot.24397] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/09/2013] [Accepted: 08/09/2013] [Indexed: 11/06/2022]
36
Valentin JB, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J, Frellsen J, Mardia KV, Tian P, Hamelryck T. Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method. Proteins 2013;82:288-99. [PMID: 23934827 DOI: 10.1002/prot.24386] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/02/2013] [Accepted: 07/18/2013] [Indexed: 01/10/2023]
37
Wang H, He Z, Zhang C, Zhang L, Xu D. Transmembrane protein alignment and fold recognition based on predicted topology. PLoS One 2013;8:e69744. [PMID: 23894534 PMCID: PMC3716705 DOI: 10.1371/journal.pone.0069744] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 06/15/2013] [Indexed: 11/18/2022]  Open
38
Lee J, Lee J. Hidden information revealed by optimal community structure from a protein-complex bipartite network improves protein function prediction. PLoS One 2013;8:e60372. [PMID: 23577106 PMCID: PMC3618231 DOI: 10.1371/journal.pone.0060372] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/25/2013] [Indexed: 11/18/2022]  Open
39
Caudron B, Jestin J. Sequence criteria for the anti-parallel character of protein beta-strands. J Theor Biol 2012;315:146-9. [DOI: 10.1016/j.jtbi.2012.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 12/17/2022]
40
Lee J, Gross SP, Lee J. Modularity optimization by conformational space annealing. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012;85:056702. [PMID: 23004898 DOI: 10.1103/physreve.85.056702] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Indexed: 06/01/2023]
41
Fan H, Periole X, Mark AE. Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models. Proteins 2012;80:1744-54. [PMID: 22411697 DOI: 10.1002/prot.24068] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 02/11/2012] [Accepted: 03/03/2012] [Indexed: 12/25/2022]
42
Cetin H, Sasaki TN, Sasai M. The Fragment-based Consistency Score in Model Quality Assessment for De Novo Prediction of Protein Structures. CHEM-BIO INFORMATICS JOURNAL 2011. [DOI: 10.1273/cbij.11.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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