Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking.

Autor: Helen M Deeks, Rebecca K Walters, Stephanie R Hare, Michael B O'Connor, Adrian J Mulholland, David R Glowacki

Publikováno v: PLoS ONE, Vol 15, Iss 3, p e0228461 (2020)

Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of interactive molecu

Externí odkaz: https://doaj.org/article/aba2e856f8de4d2a823980ea9b1932d7

Discovery of SARS-CoV-2 Mpro peptide inhibitors from modelling substrate and ligand binding

Autor: Petra Lukacik, Victor Mikhailov, Tika R. Malla, Fernanda Duarte, Rebecca M. Twidale, Claire Strain-Damerell, Alessio Lodola, Deborah K. Shoemark, Vicent Moliner, Christopher J. Schofield, Martin A. Walsh, Helen M. Deeks, Luigi Genovese, Tobias John, Rebecca K. Walters, C. David Owen, David R. Glowacki, Garrett M. Morris, James Spencer, William Dawson, Marc A. Moesser, Adrian J. Mulholland, H. T. Henry Chan, Takahito Nakajima, Eidarus Salah, Tristan Johnston-Wood, Katarzyna Świderek, Richard B. Sessions

Publikováno v: Chan, H T H, Moesser, M A, Walters, R K, Malla, T R, Twidale, R M, John, T, Deeks, H M, Johnston-Wood, T, Mikhailov, V, Sessions, R B, Dawson, W, Salah, E, Lukacik, P, Strain-Damerell, C, Owen, C D, Nakajima, T, Świderek, K, Lodola, A, Moliner, V, Glowacki, D R, Spencer, J, Walsh, M A, Schofield, C J, Genovese, L, Shoemark, D K, Mulholland, A J, Duarte, F & Morris, G M 2021, ' Discovery of SARS-CoV-2 Mpro peptide inhibitors from modelling substrate and ligand binding ', Chemical Science, vol. 12, no. 41, pp. 13686-13703 . https://doi.org/10.1039/D1SC03628A, https://doi.org/10.1039/d1sc03628a

The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and crystallographic data and an

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::50c512a698daef6740becef11c04e70c
https://research-information.bris.ac.uk/en/publications/49ca35cb-c19f-4d6d-bcab-d61edab231ca

Discovery of SARS-CoV-2 M

Autor: H T Henry, Chan, Marc A, Moesser, Rebecca K, Walters, Tika R, Malla, Rebecca M, Twidale, Tobias, John, Helen M, Deeks, Tristan, Johnston-Wood, Victor, Mikhailov, Richard B, Sessions, William, Dawson, Eidarus, Salah, Petra, Lukacik, Claire, Strain-Damerell, C David, Owen, Takahito, Nakajima, Katarzyna, Świderek, Alessio, Lodola, Vicent, Moliner, David R, Glowacki, James, Spencer, Martin A, Walsh, Christopher J, Schofield, Luigi, Genovese, Deborah K, Shoemark, Adrian J, Mulholland, Fernanda, Duarte, Garrett M, Morris

Publikováno v: Chemical Science

The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and crystallographic data and an

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::f23645c9d6dffc0b657e176904c08e7f
https://pubmed.ncbi.nlm.nih.gov/34760153

Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking

Autor: Stephanie R. Hare, Michael B. O'Connor, Adrian J. Mulholland, David R. Glowacki, Rebecca K. Walters, Helen M. Deeks

Publikováno v: Deeks, H M, Walters, R K, Hare, S R, O’Connor, M B, Mulholland, A J & Glowacki, D R 2020, ' Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking ', PLoS ONE, vol. 15, no. 3, e0228461 . https://doi.org/10.1371/journal.pone.0228461
PLoS ONE
PLoS ONE, Vol 15, Iss 3, p e0228461 (2020)

Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of interactive molecu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::03c2948d37d4f744d386e1fd791f49a4
https://research-information.bris.ac.uk/ws/files/230607350/journal.pone.0228461.pdf

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

Autor: Rebecca K. Walters, Simon J. Bennie, Robin J. Shannon, Michael B. O'Connor, Helen M. Deeks, Thomas J. Mitchell, Alex J. Jones, Alexander Jamieson-Binnie, David R. Glowacki, Adrian J. Mulholland

Publikováno v: O'Connor, M B, Bennie, S J, Deeks, H M, Jamieson-Binnie, A, Jones, A J, Shannon, R J, Walters, R, Mitchell, T J, Mulholland, A J & Glowacki, D R 2019, ' Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding : An open-source multi-person framework ', Journal of Chemical Physics, vol. 150, no. 22, 220901 . https://doi.org/10.1063/1.5092590

© 2019 Author(s). As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale diffe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fbac747b0e7f823f1bfb63d1e6549960
http://arxiv.org/abs/1902.01827