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How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β.

Intrinsically disordered proteins

Weber OC, Uversky VN.
PMID: 30250773
Intrinsically Disord Proteins. 2017 Oct 30;5(1):e1377813. doi: 10.1080/21690707.2017.1377813. eCollection 2017.

Amyloid-β

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Weber OC, Uversky VN. How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β. Intrinsically Disord Proteins. 2017;5(1):e1377813doi: 10.1080/21690707.2017.1377813.
Weber, O. C., & Uversky, V. N. (2017). How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β. Intrinsically disordered proteins, 5(1), e1377813. https://doi.org/10.1080/21690707.2017.1377813
Weber, Orkid Coskuner, and Uversky, Vladimir N. "How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β." Intrinsically disordered proteins vol. 5,1 (2017): e1377813. doi: https://doi.org/10.1080/21690707.2017.1377813
Weber OC, Uversky VN. How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β. Intrinsically Disord Proteins. 2017 Oct 30;5(1):e1377813. doi: 10.1080/21690707.2017.1377813. eCollection 2017. PMID: 30250773; PMCID: PMC6149486.
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Corrigendum: DisProt 7.0: a major update of the database of disordered proteins.

Nucleic acids research

Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC.
PMID: 27965415
Nucleic Acids Res. 2017 Jan 04;45:D1123-D1124. doi: 10.1093/nar/gkw1279. Epub 2016 Dec 13.

No abstract available.

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Piovesan D, Tabaro F, Mičetić I, et al. Corrigendum: DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res. 2016;45:D1123-D1124doi: 10.1093/nar/gkw1279.
Piovesan, D., Tabaro, F., Mičetić, I., Necci, M., Quaglia, F., Oldfield, C. J., Aspromonte, M. C., Davey, N. E., Davidović, R., Dosztányi, Z., Elofsson, A., Gasparini, A., Hatos, A., Kajava, A. V., Kalmar, L., Leonardi, E., Lazar, T., Macedo-Ribeiro, S., Macossay-Castillo, M., Meszaros, A., Minervini, G., Murvai, N., Pujols, J., Roche, D. B., Salladini, E., Schad, E., Schramm, A., Szabo, B., Tantos, A., Tonello, F., Tsirigos, K. D., Veljković, N., Ventura, S., Vranken, W., Warholm, P., Uversky, V. N., Dunker, A. K., Longhi, S., Tompa, P., & Tosatto, S. C. (2017). Corrigendum: DisProt 7.0: a major update of the database of disordered proteins. Nucleic acids research, 45D1123-D1124. https://doi.org/10.1093/nar/gkw1279
Piovesan, Damiano, et al. "Corrigendum: DisProt 7.0: a major update of the database of disordered proteins." Nucleic acids research vol. 45 (2017): D1123-D1124. doi: https://doi.org/10.1093/nar/gkw1279
Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC. Corrigendum: DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res. 2017 Jan 04;45:D1123-D1124. doi: 10.1093/nar/gkw1279. Epub 2016 Dec 13. PMID: 27965415; PMCID: PMC5210598.
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Single-cell RNA-Seq: a next generation sequencing tool for a high-resolution view of the individual cell.

Journal of biomolecular structure & dynamics

Stevenson K, Uversky VN.
PMID: 31524088
J Biomol Struct Dyn. 2020 Aug;38(12):3730-3735. doi: 10.1080/07391102.2019.1659859. Epub 2019 Sep 15.

Communicated by Ramaswamy H. Sarma.

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Stevenson K, Uversky VN. Single-cell RNA-Seq: a next generation sequencing tool for a high-resolution view of the individual cell. J Biomol Struct Dyn. 2019;38(12):3730-3735doi: 10.1080/07391102.2019.1659859.
Stevenson, K., & Uversky, V. N. (2020). Single-cell RNA-Seq: a next generation sequencing tool for a high-resolution view of the individual cell. Journal of biomolecular structure & dynamics, 38(12), 3730-3735. https://doi.org/10.1080/07391102.2019.1659859
Stevenson, Kevin, and Uversky, Vladimir N. "Single-cell RNA-Seq: a next generation sequencing tool for a high-resolution view of the individual cell." Journal of biomolecular structure & dynamics vol. 38,12 (2020): 3730-3735. doi: https://doi.org/10.1080/07391102.2019.1659859
Stevenson K, Uversky VN. Single-cell RNA-Seq: a next generation sequencing tool for a high-resolution view of the individual cell. J Biomol Struct Dyn. 2020 Aug;38(12):3730-3735. doi: 10.1080/07391102.2019.1659859. Epub 2019 Sep 15. PMID: 31524088.
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Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology.

International journal of molecular sciences

Dyakin VV, Dyakina-Fagnano NV, Mcintire LB, Uversky VN.
PMID: 35008708
Int J Mol Sci. 2021 Dec 28;23(1). doi: 10.3390/ijms23010285.

In humans, age-associated degrading changes, widely observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to...

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Dyakin VV, Dyakina-Fagnano NV, Mcintire LB, et al. Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology. Int J Mol Sci. 2021;23(1)doi: 10.3390/ijms23010285.
Dyakin, V. V., Dyakina-Fagnano, N. V., Mcintire, L. B., & Uversky, V. N. (2021). Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology. International journal of molecular sciences, 23(1), . https://doi.org/10.3390/ijms23010285
Dyakin, Victor V, et al. "Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology." International journal of molecular sciences vol. 23,1 (2021). doi: https://doi.org/10.3390/ijms23010285
Dyakin VV, Dyakina-Fagnano NV, Mcintire LB, Uversky VN. Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology. Int J Mol Sci. 2021 Dec 28;23(1). doi: 10.3390/ijms23010285. PMID: 35008708; PMCID: PMC8745688.
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Phase separation of FG-nucleoporins in nuclear pore complexes.

Biochimica et biophysica acta. Molecular cell research

Nag N, Sasidharan S, Uversky VN, Saudagar P, Tripathi T.
PMID: 34995711
Biochim Biophys Acta Mol Cell Res. 2022 Jan 04;1869(4):119205. doi: 10.1016/j.bbamcr.2021.119205. Epub 2022 Jan 04.

The nuclear envelope (NE) is a bilayer membrane that separates and physically isolates the genetic material from the cytoplasm. Nuclear pore complexes (NPCs) are cylindrical structures embedded in the NE and remain the sole channel of communication between the...

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Nag N, Sasidharan S, Uversky VN, et al. Phase separation of FG-nucleoporins in nuclear pore complexes. Biochim Biophys Acta Mol Cell Res. 2022;1869(4):119205doi: 10.1016/j.bbamcr.2021.119205.
Nag, N., Sasidharan, S., Uversky, V. N., Saudagar, P., & Tripathi, T. (2022). Phase separation of FG-nucleoporins in nuclear pore complexes. Biochimica et biophysica acta. Molecular cell research, 1869(4), 119205. https://doi.org/10.1016/j.bbamcr.2021.119205
Nag, Niharika, et al. "Phase separation of FG-nucleoporins in nuclear pore complexes." Biochimica et biophysica acta. Molecular cell research vol. 1869,4 (2022): 119205. doi: https://doi.org/10.1016/j.bbamcr.2021.119205
Nag N, Sasidharan S, Uversky VN, Saudagar P, Tripathi T. Phase separation of FG-nucleoporins in nuclear pore complexes. Biochim Biophys Acta Mol Cell Res. 2022 Jan 04;1869(4):119205. doi: 10.1016/j.bbamcr.2021.119205. Epub 2022 Jan 04. PMID: 34995711.
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A Bird's-Eye View of Proteomics.

Current protein & peptide science

Uversky VN, Alghamdi MF, Redwan EM.
PMID: 34382522
Curr Protein Pept Sci. 2021 Aug 12; doi: 10.2174/1389203722666210812120751. Epub 2021 Aug 12.

Modern protein science is broadening horizons by moving toward the systemic description of proteins in their natural habitats. This implies a transition from a classical reductionist approach associated with consideration of the unique structure and specific biological activity of...

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Uversky VN, Alghamdi MF, Redwan EM. A Bird's-Eye View of Proteomics. Curr Protein Pept Sci. 2021;doi: 10.2174/1389203722666210812120751.
Uversky, V. N., Alghamdi, M. F., & Redwan, E. M. (2021). A Bird's-Eye View of Proteomics. Current protein & peptide science, . https://doi.org/10.2174/1389203722666210812120751
Uversky, Vladimir N, et al. "A Bird's-Eye View of Proteomics." Current protein & peptide science vol. (2021). doi: https://doi.org/10.2174/1389203722666210812120751
Uversky VN, Alghamdi MF, Redwan EM. A Bird's-Eye View of Proteomics. Curr Protein Pept Sci. 2021 Aug 12; doi: 10.2174/1389203722666210812120751. Epub 2021 Aug 12. PMID: 34382522.
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Baicalein inhibits heparin-induced Tau aggregation by initializing non-toxic Tau oligomer formation.

Cell communication and signaling : CCS

Sonawane SK, Uversky VN, Chinnathambi S.
PMID: 33579328
Cell Commun Signal. 2021 Feb 12;19(1):16. doi: 10.1186/s12964-021-00704-3.

BACKGROUND: Amyloid aggregate deposition is the key feature of Alzheimer's disease. The proteinaceous aggregates found in the afflicted brain are the intra-neuronal neurofibrillary tangles formed by the microtubule-associated protein Tau and extracellular deposits, senile plaques, of amyloid beta (Aβ)...

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Sonawane SK, Uversky VN, Chinnathambi S. Baicalein inhibits heparin-induced Tau aggregation by initializing non-toxic Tau oligomer formation. Cell Commun Signal. 2021;19(1):16doi: 10.1186/s12964-021-00704-3.
Sonawane, S. K., Uversky, V. N., & Chinnathambi, S. (2021). Baicalein inhibits heparin-induced Tau aggregation by initializing non-toxic Tau oligomer formation. Cell communication and signaling : CCS, 19(1), 16. https://doi.org/10.1186/s12964-021-00704-3
Sonawane, Shweta Kishor, et al. "Baicalein inhibits heparin-induced Tau aggregation by initializing non-toxic Tau oligomer formation." Cell communication and signaling : CCS vol. 19,1 (2021): 16. doi: https://doi.org/10.1186/s12964-021-00704-3
Sonawane SK, Uversky VN, Chinnathambi S. Baicalein inhibits heparin-induced Tau aggregation by initializing non-toxic Tau oligomer formation. Cell Commun Signal. 2021 Feb 12;19(1):16. doi: 10.1186/s12964-021-00704-3. PMID: 33579328; PMCID: PMC7879681.
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Computational studies on phylogeny and drug designing using molecular simulations for COVID-19.

Journal of biomolecular structure & dynamics

Nabi F, Ahmad O, Khan YA, Nabi A, Md Amiruddin H, Abul Qais F, Masroor A, Hisamuddin M, Uversky VN, Khan RH.
PMID: 34278954
J Biomol Struct Dyn. 2021 Jul 19;1-10. doi: 10.1080/07391102.2021.1947895. Epub 2021 Jul 19.

Since the first appearance of a novel coronavirus pneumonia (NCP) caused by a novel human coronavirus, and especially after the infection started its rapid spread over the world causing the COVID-19 (coronavirus disease 2019) pandemics, a very substantial part...

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Nabi F, Ahmad O, Khan YA, et al. Computational studies on phylogeny and drug designing using molecular simulations for COVID-19. J Biomol Struct Dyn. 2021;1-10doi: 10.1080/07391102.2021.1947895.
Nabi, F., Ahmad, O., Khan, Y. A., Nabi, A., Md Amiruddin, H., Abul Qais, F., Masroor, A., Hisamuddin, M., Uversky, V. N., & Khan, R. H. (2021). Computational studies on phylogeny and drug designing using molecular simulations for COVID-19. Journal of biomolecular structure & dynamics, 1-10. https://doi.org/10.1080/07391102.2021.1947895
Nabi, Faisal, et al. "Computational studies on phylogeny and drug designing using molecular simulations for COVID-19." Journal of biomolecular structure & dynamics vol. (2021): 1-10. doi: https://doi.org/10.1080/07391102.2021.1947895
Nabi F, Ahmad O, Khan YA, Nabi A, Md Amiruddin H, Abul Qais F, Masroor A, Hisamuddin M, Uversky VN, Khan RH. Computational studies on phylogeny and drug designing using molecular simulations for COVID-19. J Biomol Struct Dyn. 2021 Jul 19;1-10. doi: 10.1080/07391102.2021.1947895. Epub 2021 Jul 19. PMID: 34278954.
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An emerging role for BAG3 in gynaecological malignancies.

British journal of cancer

De Marco M, Falco A, Iaccarino R, Raffone A, Mollo A, Guida M, Rosati A, Chetta M, Genovese G, De Caro F, Capunzo M, Turco MC, Uversky VN, Marzullo L.
PMID: 34099896
Br J Cancer. 2021 Sep;125(6):789-797. doi: 10.1038/s41416-021-01446-2. Epub 2021 Jun 07.

BAG3, a member of the BAG family of co-chaperones, is a multidomain protein with a role in several cellular processes, including the control of apoptosis, autophagy and cytoskeletal dynamics. The expression of bag3 is negligible in most cells but...

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De Marco M, Falco A, Iaccarino R, et al. An emerging role for BAG3 in gynaecological malignancies. Br J Cancer. 2021;125(6):789-797doi: 10.1038/s41416-021-01446-2.
De Marco, M., Falco, A., Iaccarino, R., Raffone, A., Mollo, A., Guida, M., Rosati, A., Chetta, M., Genovese, G., De Caro, F., Capunzo, M., Turco, M. C., Uversky, V. N., & Marzullo, L. (2021). An emerging role for BAG3 in gynaecological malignancies. British journal of cancer, 125(6), 789-797. https://doi.org/10.1038/s41416-021-01446-2
De Marco, Margot, et al. "An emerging role for BAG3 in gynaecological malignancies." British journal of cancer vol. 125,6 (2021): 789-797. doi: https://doi.org/10.1038/s41416-021-01446-2
De Marco M, Falco A, Iaccarino R, Raffone A, Mollo A, Guida M, Rosati A, Chetta M, Genovese G, De Caro F, Capunzo M, Turco MC, Uversky VN, Marzullo L. An emerging role for BAG3 in gynaecological malignancies. Br J Cancer. 2021 Sep;125(6):789-797. doi: 10.1038/s41416-021-01446-2. Epub 2021 Jun 07. PMID: 34099896; PMCID: PMC8437940.
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Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution.

Environmental research

Hassan SS, Basu P, Redwan EM, Lundstrom K, Choudhury PP, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palu G, Abd El-Aziz TM, Barh D, Uhal BD, Adadi P, Takayama K, Bazan NG, Tambuwala MM, Lal A, Chauhan G, Baetas-da-Cruz W, Sherchan SP, Uversky VN.
PMID: 34562480
Environ Res. 2022 Mar;204:112092. doi: 10.1016/j.envres.2021.112092. Epub 2021 Sep 22.

Various lineages of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have contributed to prolongation of the Coronavirus Disease 2019 (COVID-19) pandemic. Several non-synonymous mutations in SARS-CoV-2 proteins have generated multiple SARS-CoV-2 variants. In our previous report, we have shown that...

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Hassan SS, Basu P, Redwan EM, et al. Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution. Environ Res. 2021;204:112092doi: 10.1016/j.envres.2021.112092.
Hassan, S. S., Basu, P., Redwan, E. M., Lundstrom, K., Choudhury, P. P., Serrano-Aroca, �. �., Azad, G. K., Aljabali, A. A. A., Palu, G., Abd El-Aziz, T. M., Barh, D., Uhal, B. D., Adadi, P., Takayama, K., Bazan, N. G., Tambuwala, M. M., Lal, A., Chauhan, G., Baetas-da-Cruz, W., Sherchan, S. P., & Uversky, V. N. (2022). Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution. Environmental research, 204112092. https://doi.org/10.1016/j.envres.2021.112092
Hassan, Sk Sarif, et al. "Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution." Environmental research vol. 204 (2022): 112092. doi: https://doi.org/10.1016/j.envres.2021.112092
Hassan SS, Basu P, Redwan EM, Lundstrom K, Choudhury PP, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palu G, Abd El-Aziz TM, Barh D, Uhal BD, Adadi P, Takayama K, Bazan NG, Tambuwala MM, Lal A, Chauhan G, Baetas-da-Cruz W, Sherchan SP, Uversky VN. Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution. Environ Res. 2022 Mar;204:112092. doi: 10.1016/j.envres.2021.112092. Epub 2021 Sep 22. PMID: 34562480; PMCID: PMC8457672.
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DeepA-RBPBS: A hybrid convolution and recurrent neural network combined with attention mechanism for predicting RBP binding site.

Journal of biomolecular structure & dynamics

Du Z, Xiao X, Uversky VN.
PMID: 33272122
J Biomol Struct Dyn. 2020 Dec 04;1-9. doi: 10.1080/07391102.2020.1854861. Epub 2020 Dec 04.

It's important to infer the binding site of RNA-binding proteins (RBP) for understanding the interaction between RBP and its RNA targets and decipher the mechanisms of transcriptional regulation. However, experimental detection of RBP binding sites is still time-intensive and...

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Du Z, Xiao X, Uversky VN. DeepA-RBPBS: A hybrid convolution and recurrent neural network combined with attention mechanism for predicting RBP binding site. J Biomol Struct Dyn. 2020;1-9doi: 10.1080/07391102.2020.1854861.
Du, Z., Xiao, X., & Uversky, V. N. (2020). DeepA-RBPBS: A hybrid convolution and recurrent neural network combined with attention mechanism for predicting RBP binding site. Journal of biomolecular structure & dynamics, 1-9. https://doi.org/10.1080/07391102.2020.1854861
Du, Zhihua, et al. "DeepA-RBPBS: A hybrid convolution and recurrent neural network combined with attention mechanism for predicting RBP binding site." Journal of biomolecular structure & dynamics vol. (2020): 1-9. doi: https://doi.org/10.1080/07391102.2020.1854861
Du Z, Xiao X, Uversky VN. DeepA-RBPBS: A hybrid convolution and recurrent neural network combined with attention mechanism for predicting RBP binding site. J Biomol Struct Dyn. 2020 Dec 04;1-9. doi: 10.1080/07391102.2020.1854861. Epub 2020 Dec 04. PMID: 33272122.
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On the origin of matrix mechanism in protocells and key problems of molecular biology.

Journal of biomolecular structure & dynamics

Kostetsky EY, Uversky VN.
PMID: 32820704
J Biomol Struct Dyn. 2020 Aug 21;1-12. doi: 10.1080/07391102.2020.1809523. Epub 2020 Aug 21.

The theory of the emergence of the matrix mechanism in protocells on complexes of minerals (apatite, carbonate-apatite, calcite, and quartz) with the reciprocal proportions and with the participation of the gas phase radicals (NH3, CH4, and CO) is considered....

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Kostetsky EY, Uversky VN. On the origin of matrix mechanism in protocells and key problems of molecular biology. J Biomol Struct Dyn. 2020;1-12doi: 10.1080/07391102.2020.1809523.
Kostetsky, E. Y., & Uversky, V. N. (2020). On the origin of matrix mechanism in protocells and key problems of molecular biology. Journal of biomolecular structure & dynamics, 1-12. https://doi.org/10.1080/07391102.2020.1809523
Kostetsky, Eduard Y, and Uversky, Vladimir N. "On the origin of matrix mechanism in protocells and key problems of molecular biology." Journal of biomolecular structure & dynamics vol. (2020): 1-12. doi: https://doi.org/10.1080/07391102.2020.1809523
Kostetsky EY, Uversky VN. On the origin of matrix mechanism in protocells and key problems of molecular biology. J Biomol Struct Dyn. 2020 Aug 21;1-12. doi: 10.1080/07391102.2020.1809523. Epub 2020 Aug 21. PMID: 32820704.
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