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For: Khoury GA, Smadbeck J, Tamamis P, Vandris AC, Kieslich CA, Floudas CA. Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family. ACS Synth Biol 2014;3:855-69. [PMID: 24932669 DOI: 10.1021/sb400168u] [Cited by in Crossref: 48] [Cited by in F6Publishing: 46] [Article Influence: 6.0] [Reference Citation Analysis]
Number Citing Articles
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2 Wang Q, Zhao WC, Fu XQ, Zheng QC. Exploring the Distinct Binding and Activation Mechanisms for Different CagA Oncoproteins and SHP2 by Molecular Dynamics Simulations. Molecules 2021;26:837. [PMID: 33562680 DOI: 10.3390/molecules26040837] [Reference Citation Analysis]
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4 Khoury GA, Bhatia N, Floudas CA. Hydration free energies calculated using the AMBER ff03 charge model for natural and unnatural amino acids and multiple water models. Computers & Chemical Engineering 2014;71:745-52. [DOI: 10.1016/j.compchemeng.2014.07.017] [Cited by in Crossref: 7] [Cited by in F6Publishing: 1] [Article Influence: 0.9] [Reference Citation Analysis]
5 Giannakoulias S, Shringari SR, Ferrie JJ, Petersson EJ. Biomolecular simulation based machine learning models accurately predict sites of tolerability to the unnatural amino acid acridonylalanine. Sci Rep 2021;11:18406. [PMID: 34526629 DOI: 10.1038/s41598-021-97965-2] [Reference Citation Analysis]
6 Akter R, Zou J, Raleigh DP. Differential effects of serine side chain interactions in amyloid formation by islet amyloid polypeptide. Protein Sci 2020;29:555-63. [PMID: 31705766 DOI: 10.1002/pro.3782] [Cited by in Crossref: 2] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
7 Kamenik AS, Lessel U, Fuchs JE, Fox T, Liedl KR. Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization. J Chem Inf Model 2018;58:982-92. [PMID: 29652495 DOI: 10.1021/acs.jcim.8b00097] [Cited by in Crossref: 32] [Cited by in F6Publishing: 28] [Article Influence: 8.0] [Reference Citation Analysis]
8 Welker Leng KR, Castañeda CA, Decroos C, Islam B, Haider SM, Christianson DW, Fierke CA. Phosphorylation of Histone Deacetylase 8: Structural and Mechanistic Analysis of the Phosphomimetic S39E Mutant. Biochemistry 2019;58:4480-93. [PMID: 31633931 DOI: 10.1021/acs.biochem.9b00653] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 1.3] [Reference Citation Analysis]
9 Schaub AJ, Moreno GO, Zhao S, Truong HV, Luo R, Tsai SC. Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases. Methods Enzymol 2019;622:375-409. [PMID: 31155062 DOI: 10.1016/bs.mie.2019.03.001] [Cited by in Crossref: 4] [Cited by in F6Publishing: 3] [Article Influence: 1.3] [Reference Citation Analysis]
10 Bertozo LDC, Maszota-zieleniak M, Bolean M, Ciancaglini P, Samsonov SA, Ximenes VF. Binding of fluorescent dansyl amino acids in albumin: When access to the protein cavity is more important than the strength of binding. Dyes and Pigments 2021;188:109195. [DOI: 10.1016/j.dyepig.2021.109195] [Cited by in Crossref: 3] [Cited by in F6Publishing: 2] [Article Influence: 3.0] [Reference Citation Analysis]
11 Garton M, Corbi-Verge C, Hu Y, Nim S, Tarasova N, Sherborne B, Kim PM. Rapid and accurate structure-based therapeutic peptide design using GPU accelerated thermodynamic integration. Proteins 2019;87:236-44. [PMID: 30520126 DOI: 10.1002/prot.25644] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
12 Nagaoka K, Mei H, Guo Y, Han J, Konno H, Moriwaki H, Soloshonok VA. Michael addition reactions of chiral glycine Schiff base Ni (II)‐complex with 1‐(1‐phenylsulfonyl)benzene. Chirality 2020;32:885-93. [DOI: 10.1002/chir.23203] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 2.0] [Reference Citation Analysis]
13 Krebs SK, Rakotoarinoro N, Stech M, Zemella A, Kubick S. A CHO-Based Cell-Free Dual Fluorescence Reporter System for the Straightforward Assessment of Amber Suppression and scFv Functionality. Front Bioeng Biotechnol 2022;10:873906. [DOI: 10.3389/fbioe.2022.873906] [Reference Citation Analysis]
14 Wang Q, Zheng Q, Zhang H. Exploring the mechanism how AF9 recognizes and binds H3K9ac by molecular dynamics simulations and free energy calculations: Mechanism How AF9 Recognizes and Binds H3K9ac. Biopolymers 2016;105:779-86. [DOI: 10.1002/bip.22896] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 0.8] [Reference Citation Analysis]
15 Orr AA, Wördehoff MM, Hoyer W, Tamamis P. Uncovering the Binding and Specificity of β-Wrapins for Amyloid-β and α-Synuclein. J Phys Chem B 2016;120:12781-94. [DOI: 10.1021/acs.jpcb.6b08485] [Cited by in Crossref: 16] [Cited by in F6Publishing: 16] [Article Influence: 2.7] [Reference Citation Analysis]
16 Wang X, Li W. Development and Testing of Force Field Parameters for Phenylalanine and Tyrosine Derivatives. Front Mol Biosci 2020;7:608931. [PMID: 33385013 DOI: 10.3389/fmolb.2020.608931] [Reference Citation Analysis]
17 Watkins AM, Arora PS. Structure-based inhibition of protein-protein interactions. Eur J Med Chem 2015;94:480-8. [PMID: 25253637 DOI: 10.1016/j.ejmech.2014.09.047] [Cited by in Crossref: 36] [Cited by in F6Publishing: 31] [Article Influence: 4.5] [Reference Citation Analysis]
18 Zhou S, Wang Q, Ren M, Zhang A, Liu H, Yao X. Molecular dynamics simulation on the inhibition mechanism of peptide-based inhibitor of islet amyloid polypeptide (IAPP) to islet amyloid polypeptide (IAPP 22-28 ) oligomers. Chem Biol Drug Des 2017;90:31-9. [DOI: 10.1111/cbdd.12924] [Cited by in Crossref: 6] [Cited by in F6Publishing: 5] [Article Influence: 1.2] [Reference Citation Analysis]
19 Wang X, Zheng Q. Theoretical research in structure characteristics of different inhibitors and differences of binding modes with CBP bromodomain. Bioorganic & Medicinal Chemistry 2018;26:712-20. [DOI: 10.1016/j.bmc.2017.12.040] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 1.3] [Reference Citation Analysis]
20 Mu J, Zhou J, Gong Q, Xu Q. An allosteric regulation mechanism of Arabidopsis Serine/Threonine kinase 1 (SIK1) through phosphorylation. Computational and Structural Biotechnology Journal 2022;20:368-79. [DOI: 10.1016/j.csbj.2021.12.033] [Reference Citation Analysis]
21 Liou S, Chuo S, Qiu Y, Wang L, Goodin DB. Linkage between Proximal and Distal Movements of P450cam Induced by Putidaredoxin. Biochemistry 2020;59:2012-21. [DOI: 10.1021/acs.biochem.0c00294] [Cited by in Crossref: 5] [Cited by in F6Publishing: 4] [Article Influence: 2.5] [Reference Citation Analysis]
22 Qvit N, Rubin SJS, Urban TJ, Mochly-Rosen D, Gross ER. Peptidomimetic therapeutics: scientific approaches and opportunities. Drug Discov Today 2017;22:454-62. [PMID: 27856346 DOI: 10.1016/j.drudis.2016.11.003] [Cited by in Crossref: 116] [Cited by in F6Publishing: 99] [Article Influence: 19.3] [Reference Citation Analysis]
23 Orr AA, Kuhlmann SK, Tamamis P. Computational design of a β-wrapin's N-terminal domain with canonical and non-canonical amino acid modifications mimicking curcumin's proposed inhibitory function. Biophysical Chemistry 2022. [DOI: 10.1016/j.bpc.2022.106805] [Reference Citation Analysis]
24 Orr AA, Jayaraman A, Tamamis P. Molecular Modeling of Chemoreceptor:Ligand Interactions. Methods Mol Biol 2018;1729:353-72. [PMID: 29429104 DOI: 10.1007/978-1-4939-7577-8_28] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 1.0] [Reference Citation Analysis]
25 Mathur D, Prakash S, Anand P, Kaur H, Agrawal P, Mehta A, Kumar R, Singh S, Raghava GP. PEPlife: A Repository of the Half-life of Peptides. Sci Rep 2016;6:36617. [PMID: 27819351 DOI: 10.1038/srep36617] [Cited by in Crossref: 65] [Cited by in F6Publishing: 53] [Article Influence: 10.8] [Reference Citation Analysis]
26 Shi X, Chuo S, Liou S, Goodin DB. Double Electron–Electron Resonance Shows That the Substrate but Not the Inhibitors Causes Disorder in the F/G Loop of CYP119 in Solution. Biochemistry 2020;59:1823-31. [DOI: 10.1021/acs.biochem.0c00171] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.5] [Reference Citation Analysis]
27 Blasco P, Zhang C, Chow HY, Chen G, Wu Y, Li X. An atomic perspective on improving daptomycin's activity. Biochim Biophys Acta Gen Subj 2021;1865:129918. [PMID: 33965439 DOI: 10.1016/j.bbagen.2021.129918] [Reference Citation Analysis]
28 Żesławska E, Jakubowska A, Nitek W. Conformational study of the 3,6-dihydro-2H-1,4-oxazin-2-one fragment in 8-tert-butyl-7-methoxy-8-methyl-9-oxa-6-azaspiro[4.5]decane-2,10-dione stereoisomers. Acta Crystallogr C Struct Chem 2017;73:556-62. [PMID: 28677608 DOI: 10.1107/S2053229617009068] [Reference Citation Analysis]
29 Wang Q, Zhao WC, Fu XQ, Zheng QC. Exploring the Allosteric Mechanism of Src Homology-2 Domain-Containing Protein Tyrosine Phosphatase 2 (SHP2) by Molecular Dynamics Simulations. Front Chem 2020;8:597495. [PMID: 33330386 DOI: 10.3389/fchem.2020.597495] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.5] [Reference Citation Analysis]
30 Reinhardt CR, Sequeira R, Tommos C, Hammes-Schiffer S. Computing Proton-Coupled Redox Potentials of Fluorotyrosines in a Protein Environment. J Phys Chem B 2021;125:128-36. [PMID: 33378205 DOI: 10.1021/acs.jpcb.0c09974] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
31 Singh S, Singh H, Tuknait A, Chaudhary K, Singh B, Kumaran S, Raghava GP. PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues. Biol Direct 2015;10:73. [PMID: 26690490 DOI: 10.1186/s13062-015-0103-4] [Cited by in Crossref: 80] [Cited by in F6Publishing: 75] [Article Influence: 11.4] [Reference Citation Analysis]
32 Perez A, Sittel F, Stock G, Dill K. MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths. J Chem Theory Comput 2018;14:2109-16. [PMID: 29547695 DOI: 10.1021/acs.jctc.7b01294] [Cited by in Crossref: 7] [Cited by in F6Publishing: 6] [Article Influence: 1.8] [Reference Citation Analysis]
33 Singh S, Chaudhary K, Dhanda SK, Bhalla S, Usmani SS, Gautam A, Tuknait A, Agrawal P, Mathur D, Raghava GP. SATPdb: a database of structurally annotated therapeutic peptides. Nucleic Acids Res 2016;44:D1119-26. [PMID: 26527728 DOI: 10.1093/nar/gkv1114] [Cited by in Crossref: 67] [Cited by in F6Publishing: 61] [Article Influence: 9.6] [Reference Citation Analysis]
34 Tyagi A, Tuknait A, Anand P, Gupta S, Sharma M, Mathur D, Joshi A, Singh S, Gautam A, Raghava GP. CancerPPD: a database of anticancer peptides and proteins. Nucleic Acids Res 2015;43:D837-43. [PMID: 25270878 DOI: 10.1093/nar/gku892] [Cited by in Crossref: 129] [Cited by in F6Publishing: 116] [Article Influence: 16.1] [Reference Citation Analysis]
35 Zhou R, Pan Z, Zhang Y, Wu F, Jiang Q, Guo L. Base-Promoted Synthesis of β-Substituted-Tryptophans via a Simple and Convenient Three-Component Condensation of Nickel(II) Glycinate. Molecules 2017;22:E695. [PMID: 28448432 DOI: 10.3390/molecules22050695] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.2] [Reference Citation Analysis]
36 Jakubowska A, Żuchowski G, Kulig K. Cyclic sulfates as useful tools in the asymmetric synthesis of 1-aminocyclopropane-1-carboxylic acid derivatives. Tetrahedron: Asymmetry 2015;26:1261-7. [DOI: 10.1016/j.tetasy.2015.09.013] [Cited by in Crossref: 5] [Cited by in F6Publishing: 1] [Article Influence: 0.7] [Reference Citation Analysis]
37 Shkurti A, Styliari ID, Balasubramanian V, Bethune I, Pedebos C, Jha S, Laughton CA. CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space. J Chem Theory Comput 2019;15:2587-96. [PMID: 30620585 DOI: 10.1021/acs.jctc.8b00657] [Cited by in Crossref: 10] [Cited by in F6Publishing: 10] [Article Influence: 3.3] [Reference Citation Analysis]
38 Itang CEMM, Gaza JT, Masacupan DJM, Batoctoy DCR, Chen YJ, Nellas RB, Yu ET. Identification of Conomarphin Variants in the Conus eburneus Venom and the Effect of Sequence and PTM Variations on Conomarphin Conformations. Mar Drugs 2020;18:E503. [PMID: 33019526 DOI: 10.3390/md18100503] [Reference Citation Analysis]
39 Orr AA, Shaykhalishahi H, Mirecka EA, Jonnalagadda SVR, Hoyer W, Tamamis P. Elucidating the multi-targeted anti-amyloid activity and enhanced islet amyloid polypeptide binding of β-wrapins. Comput Chem Eng 2018;116:322-32. [PMID: 30405276 DOI: 10.1016/j.compchemeng.2018.02.013] [Cited by in Crossref: 9] [Cited by in F6Publishing: 8] [Article Influence: 2.3] [Reference Citation Analysis]
40 Holden JK, Pavlovicz R, Gobbi A, Song Y, Cunningham CN. Computational Site Saturation Mutagenesis of Canonical and Non-Canonical Amino Acids to Probe Protein-Peptide Interactions. Front Mol Biosci 2022;9:848689. [DOI: 10.3389/fmolb.2022.848689] [Reference Citation Analysis]
41 Orr AA, Gonzalez-rivera JC, Wilson M, Bhikha PR, Wang D, Contreras LM, Tamamis P. A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins. Methods 2018;143:34-47. [DOI: 10.1016/j.ymeth.2018.01.015] [Cited by in Crossref: 6] [Cited by in F6Publishing: 6] [Article Influence: 1.5] [Reference Citation Analysis]
42 Guardiola S, Díaz-lobo M, Seco J, García J, Nevola L, Giralt E. Peptides Targeting EGF Block the EGF-EGFR Interaction. ChemBioChem 2016;17:702-11. [DOI: 10.1002/cbic.201500525] [Cited by in Crossref: 14] [Cited by in F6Publishing: 12] [Article Influence: 2.3] [Reference Citation Analysis]
43 Perdikari TM, Jovic N, Dignon GL, Kim YC, Fawzi NL, Mittal J. A predictive coarse-grained model for position-specific effects of post-translational modifications. Biophys J 2021;120:1187-97. [PMID: 33582133 DOI: 10.1016/j.bpj.2021.01.034] [Cited by in Crossref: 11] [Cited by in F6Publishing: 10] [Article Influence: 11.0] [Reference Citation Analysis]
44 Agrawal P, Bhalla S, Usmani SS, Singh S, Chaudhary K, Raghava GP, Gautam A. CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides. Nucleic Acids Res 2016;44:D1098-103. [PMID: 26586798 DOI: 10.1093/nar/gkv1266] [Cited by in Crossref: 142] [Cited by in F6Publishing: 119] [Article Influence: 20.3] [Reference Citation Analysis]
45 Gorham RD Jr, Forest DL, Khoury GA, Smadbeck J, Beecher CN, Healy ED, Tamamis P, Archontis G, Larive CK, Floudas CA, Radeke MJ, Johnson LV, Morikis D. New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. J Med Chem 2015;58:814-26. [PMID: 25494040 DOI: 10.1021/jm501345y] [Cited by in Crossref: 13] [Cited by in F6Publishing: 11] [Article Influence: 1.6] [Reference Citation Analysis]
46 Ono S, Naylor MR, Townsend CE, Okumura C, Okada O, Lee HW, Lokey RS. Cyclosporin A: Conformational Complexity and Chameleonicity. J Chem Inf Model 2021;61:5601-13. [PMID: 34672629 DOI: 10.1021/acs.jcim.1c00771] [Reference Citation Analysis]