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 …

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 …

Serum albumin domain structures in human blood serum by mass spectrometry and computational biology

A Belsom, M Schneider, L Fischer, O Brock… - Molecular & Cellular …, 2016 - ASBMB
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 …

Structure and dynamics of the huntingtin exon-1 N-terminus: a solution NMR perspective

M Baias, PES Smith, K Shen… - Journal of the …, 2017 - ACS Publications
Many neurodegenerative diseases are characterized by misfolding and aggregation of an
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

L Rozano, YM Mukuka, JK Hane… - International Journal of …, 2023 - mdpi.com
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 …

Prediction of intrinsic disorder using Rosetta ResidueDisorder and AlphaFold2

J He, SMBA Turzo, JT Seffernick, SS Kim… - The Journal of …, 2022 - ACS Publications
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 …

ATP transport through VDAC and the VDAC–tubulin complex probed by equilibrium and Nonequilibrium MD simulations

SY Noskov, TK Rostovtseva, SM Bezrukov - Biochemistry, 2013 - ACS Publications
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 …

Protein language models: is scaling necessary?

Q Fournier, RM Vernon, A van der Sloot, B Schulz… - bioRxiv, 2024 - biorxiv.org
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 …

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 …

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 …