A structural biology community assessment of AlphaFold2 applications

Autor: Akdel, Mehmet, Pires, Douglas EV, Pardo, Eduard Porta, Jänes, Jürgen, Zalevsky, Arthur O, Mészáros, Bálint, Bryant, Patrick, Good, Lydia L, Laskowski, Roman A, Pozzati, Gabriele, Shenoy, Aditi, Zhu, Wensi, Kundrotas, Petras, Serra, Victoria Ruiz, Rodrigues, Carlos HM, Dunham, Alistair S, Burke, David, Borkakoti, Neera, Velankar, Sameer, Frost, Adam, Basquin, Jérôme, Lindorff-Larsen, Kresten, Bateman, Alex, Kajava, Andrey V, Valencia, Alfonso, Ovchinnikov, Sergey, Durairaj, Janani, Ascher, David B, Thornton, Janet M, Davey, Norman E, Stein, Amelie, Elofsson, Arne, Croll, Tristan I, Beltrao, Pedro

Publikováno v: Nature Structural & Molecular Biology, 29 (11)
Akdel, M, Pires, D E, Porta Pardo, E, Jänes, J, Zalevsky, A O, Meszaros, B, Bryant, P, Good, L L, Laskowski, R A, Pozzati, G, Shenoy, A, Zhu, W, Kundrotas, P, Serra, V R, Rodrigues, C H M, Dunham, A S, Burke, D, Borkakoti, N, Velankar, S, Frost, A, Basquin, J, Lindorff-Larsen, K, Bateman, A, Kajava, A, Valencia, A, Ovchinnikov, S, Durairaj, J, Ascher, D B, Thornton, J M, Davey, N E, Stein, A, Elofsson, A, Croll, T & Beltrao, P 2022, ' A structural biology community assessment of AlphaFold2 applications ', Nature Structural & Molecular Biology, vol. 29, no. 11 . https://doi.org/10.1038/s41594-022-00849-w
Nature Structural and Molecular Biology 29 (2022) 11
Nature Structural and Molecular Biology, 29(11), 1056-1067

Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally de

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::56b5120d87bb9bff7ff683ea7fd4c584

mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions

Autor: Rodrigues, Carlos HM, Pires, Douglas EV, Ascher, David B

Protein-protein interactions play a crucial role in all cellular functions and biological processes and mutations leading to their disruption are enriched in many diseases. While a number of computational methods to assess the effects of variants on

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::366891c3ffd8665d5ca699bc697fdef0

mCSM-PPI2: predicting the effects of mutations on protein-protein interactions

Autor: Rodrigues, Carlos HM, Myung, Yoochan, Pires, Douglas EV, Ascher, David B

Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predic

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::92fad3743c908f3d24d4d900f9d0c49b
https://www.repository.cam.ac.uk/handle/1810/292839

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

Autor: Rodrigues, Carlos HM, Pires, Douglas EV, Ascher, David B

Publikováno v: Nucleic Acids Research

Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based approaches for assessing the i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::64b4fbfe5abbb540a2f86e61466eab4d

mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance

Autor: Pires, Douglas EV, Blundell, Tom L, Ascher, David B

Publikováno v: Scientific Reports

The ability to predict how a mutation affects ligand binding is an essential step in understanding, anticipating and improving the design of new treatments for drug resistance, and in understanding genetic diseases. Here we present mCSM-lig, a struct

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::35fdbc3e172576fb741c721faba99bc9