Principles and overview of sampling methods for modeling macromolecular structure and dynamics
T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …
how macromolecules carry out their functions in the cell. Significant advances have been …
Recent advances in NMR protein structure prediction with ROSETTA
J Koehler Leman, G Künze - International Journal of Molecular Sciences, 2023 - mdpi.com
Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for studying the
structure and dynamics of proteins in their native state. For high-resolution NMR structure …
structure and dynamics of proteins in their native state. For high-resolution NMR structure …
Serum albumin domain structures in human blood serum by mass spectrometry and computational biology
Chemical cross-linking combined with mass spectrometry has proven useful for studying
protein-protein interactions and protein structure, however the low density of cross-link data …
protein-protein interactions and protein structure, however the low density of cross-link data …
Structure and dynamics of the huntingtin exon-1 N-terminus: a solution NMR perspective
Many neurodegenerative diseases are characterized by misfolding and aggregation of an
expanded polyglutamine tract (polyQ). Huntington's Disease, caused by expansion of the …
expanded polyglutamine tract (polyQ). Huntington's Disease, caused by expansion of the …
Ab initio modelling of the structure of ToxA-like and MAX fungal effector proteins
Pathogenic fungal diseases in crops are mediated by the release of effector proteins that
facilitate infection. Characterising the structure of these fungal effectors is vital to …
facilitate infection. Characterising the structure of these fungal effectors is vital to …
Prediction of intrinsic disorder using Rosetta ResidueDisorder and AlphaFold2
The combination of deep learning and sequence data has transformed protein structure
prediction and modeling, evidenced in the success of AlphaFold (AF). For this reason, many …
prediction and modeling, evidenced in the success of AlphaFold (AF). For this reason, many …
ATP transport through VDAC and the VDAC–tubulin complex probed by equilibrium and Nonequilibrium MD simulations
Voltage-dependent anion channel (VDAC), the major channel of the mitochondrial outer
membrane, serves as a principal pathway for ATP, ADP, and other respiratory substrates …
membrane, serves as a principal pathway for ATP, ADP, and other respiratory substrates …
Protein language models: is scaling necessary?
Public protein sequence databases contain samples from the fitness landscape explored by
nature. Protein language models (pLMs) pre-trained on these sequences aim to capture this …
nature. Protein language models (pLMs) pre-trained on these sequences aim to capture this …
Isoform-specific interactions of the von Hippel-Lindau tumor suppressor protein
G Minervini, GM Mazzotta, A Masiero, E Sartori… - Scientific Reports, 2015 - nature.com
Deregulation of the von Hippel-Lindau tumor suppressor protein (pVHL) is considered one
of the main causes for malignant renal clear-cell carcinoma (ccRCC) insurgence. In human …
of the main causes for malignant renal clear-cell carcinoma (ccRCC) insurgence. In human …
A unified de novo approach for predicting the structures of ordered and disordered proteins
JJ Ferrie, EJ Petersson - The Journal of Physical Chemistry B, 2020 - ACS Publications
As recognition of the abundance and relevance of intrinsically disordered proteins (IDPs)
continues to grow, demand increases for methods that can rapidly predict the conformational …
continues to grow, demand increases for methods that can rapidly predict the conformational …