Toward the solution of the protein structure prediction problem
Since Anfinsen demonstrated that the information encoded in a protein's amino acid
sequence determines its structure in 1973, solving the protein structure prediction problem …
sequence determines its structure in 1973, solving the protein structure prediction problem …
Protein design via deep learning
Proteins with desired functions and properties are important in fields like nanotechnology
and biomedicine. De novo protein design enables the production of previously unseen …
and biomedicine. De novo protein design enables the production of previously unseen …
[HTML][HTML] The human urine metabolome
S Bouatra, F Aziat, R Mandal, AC Guo, MR Wilson… - PloS one, 2013 - journals.plos.org
Urine has long been a “favored” biofluid among metabolomics researchers. It is sterile, easy-
to-obtain in large volumes, largely free from interfering proteins or lipids and chemically …
to-obtain in large volumes, largely free from interfering proteins or lipids and chemically …
STRUM: structure-based prediction of protein stability changes upon single-point mutation
L Quan, Q Lv, Y Zhang - Bioinformatics, 2016 - academic.oup.com
Motivation: Mutations in human genome are mainly through single nucleotide
polymorphism, some of which can affect stability and function of proteins, causing human …
polymorphism, some of which can affect stability and function of proteins, causing human …
Protein structure prediction: when is it useful?
Y Zhang - Current opinion in structural biology, 2009 - Elsevier
Computationally predicted three-dimensional structure of protein molecules has
demonstrated the usefulness in many areas of biomedicine, ranging from approximate …
demonstrated the usefulness in many areas of biomedicine, ranging from approximate …
PIPs: human protein–protein interaction prediction database
Abstract The PIPs database (http://www. compbio. dundee. ac. uk/www-pips) is a resource
for studying protein–protein interactions in human. It contains predictions of> 37 000 high …
for studying protein–protein interactions in human. It contains predictions of> 37 000 high …
Molecular docking screens using comparative models of proteins
Two orders of magnitude more protein sequences can be modeled by comparative
modeling than have been determined by X-ray crystallography and NMR spectroscopy …
modeling than have been determined by X-ray crystallography and NMR spectroscopy …
Exploring protein dynamics space: the dynasome as the missing link between protein structure and function
Proteins are usually described and classified according to amino acid sequence, structure or
function. Here, we develop a minimally biased scheme to compare and classify proteins …
function. Here, we develop a minimally biased scheme to compare and classify proteins …
The NAD+ salvage pathway supports PHGDH-driven serine biosynthesis
JP Murphy, MA Giacomantonio, JA Paulo, RA Everley… - Cell reports, 2018 - cell.com
NAD+ is a key metabolic redox cofactor that is regenerated from nicotinamide through the
NAD+ salvage pathway. Here, we find that inhibiting the NAD+ salvage pathway depletes …
NAD+ salvage pathway. Here, we find that inhibiting the NAD+ salvage pathway depletes …
Accurate and fast prediction of intrinsically disordered protein by multiple protein language models and ensemble learning
S Xu, A Onoda - Journal of Chemical Information and Modeling, 2023 - ACS Publications
Intrinsically disordered proteins (IDPs) play a vital role in various biological processes and
have attracted increasing attention in the past few decades. Predicting IDPs from the primary …
have attracted increasing attention in the past few decades. Predicting IDPs from the primary …