381 citations · 1k across the 13 of their papers we have counts for
13 papers
Deep Learning of Proteins with Local and Global Regions of Disorder
Oufan Zhang, Zi Hao Liu, Julie D Forman-Kay +1
Although machine learning has transformed protein structure prediction of folded protein ground states with remarkable accuracy, intrinsically disordered proteins and regions (IDPs…
Biological Insights from Integrative Modeling of Intrinsically Disordered Protein Systems
Zi Hao Liu, Maria Tsanai, Oufan Zhang +2
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short re…
Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes
Zi Hao Liu, Maria Tsanai, Oufan Zhang +2
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under phy…
A Curated Rotamer Library for Common Post-Translational Modifications of Proteins
Oufan Zhang, Shubhankar A. Naik, Zi Hao Liu +2
Sidechain rotamer libraries of the common amino acids of a protein are useful for folded protein structure determination and for generating ensembles of intrinsically disordered pr…
Electrostatics of Salt-Dependent Reentrant Phase Behaviors Highlights Diverse Roles of ATP in Biomolecular Condensates
Yi-Hsuan Lin, Tae Hun Kim, Suman Das +6
Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The…
Learning to Evolve Structural Ensembles of Unfolded and Disordered Proteins Using Experimental Solution Data
Oufan Zhang, Mojtaba Haghighatlari, Jie Li +5
We have developed a Generative Recurrent Neural Networks (GRNN) that learns the probability of the next residue torsions from the pre…
Learning Correlations between Internal Coordinates to improve 3D Cartesian Coordinates for Proteins
Jie Li, Oufan Zhang, Seokyoung Lee +5
We consider a generic representation problem of internal coordinates (bond lengths, valence angles, and dihedral angles) and their transformation to 3-dimensional Cartesian coordin…
Configurational Entropy of Folded Proteins and its Importance for Intrinsically Disordered Proteins
Meili Liu, Akshaya K. Das, James Lincoff +5
Many pairwise additive force fields are in active use for intrinsically disordered proteins (IDPs) and regions (IDRs), some of which modify energetic terms to improve description o…
Comparative Roles of Charge, and Hydrophobic Interactions in Sequence-Dependent Phase Separation of Intrinsically Disordered Proteins
Suman Das, Yi-Hsuan Lin, Robert M. Vernon +2
Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular condensates underlain by liquid-liquid phase separation (LLPS), we conducted mult…
Extended Experimental Inferential Structure Determination Method for Evaluating the Structural Ensembles of Disordered Protein States
James Lincoff, Mickael Krzeminski, Mojtaba Haghighatlari +5
Characterization of proteins with intrinsic or unfolded state disorder comprises a new frontier in structural biology, requiring the characterization of diverse and dynamic structu…
Charge Pattern Matching as a "Fuzzy" Mode of Molecular Recognition for the Functional Phase Separations of Intrinsically Disordered Proteins
Yi-Hsuan Lin, Jacob P. Brady, Julie D. Forman-Kay +1
Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is curren…
Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteins
Yi-Hsuan Lin, Jianhui Song, Julie D. Forman-Kay +1
Intrinsically disordered proteins (IDPs) are typically low in nonpolar/hydrophobic but relatively high in polar, charged, and aromatic amino acid compositions. Some IDPs undergo li…
Sequence-specific polyampholyte phase separation in membraneless organelles
Yi-Hsuan Lin, Julie D. Forman-Kay, Hue Sun Chan
Liquid-liquid phase separation of charge/aromatic-enriched intrinsically disordered proteins (IDPs) is critical in the biological function of membraneless organelles. Much of the p…