Using PyMOL as a platform for computational drug design
PyMOL, a cross‐platform molecular graphics tool, has been widely used for three‐
dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron …
dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron …
Phytochrome structure and signaling mechanisms
NC Rockwell, YS Su, JC Lagarias - Annu. Rev. Plant Biol., 2006 - annualreviews.org
Phytochromes are a widespread family of red/far-red responsive photoreceptors first
discovered in plants, where they constitute one of the three main classes of …
discovered in plants, where they constitute one of the three main classes of …
Illuminating protein space with a programmable generative model
Three billion years of evolution has produced a tremendous diversity of protein molecules,
but the full potential of proteins is likely to be much greater. Accessing this potential has …
but the full potential of proteins is likely to be much greater. Accessing this potential has …
De novo design of protein interactions with learned surface fingerprints
Physical interactions between proteins are essential for most biological processes
governing life. However, the molecular determinants of such interactions have been …
governing life. However, the molecular determinants of such interactions have been …
Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations
Structure prediction for proteins lacking homologous templates in the Protein Data Bank
(PDB) remains a significant unsolved problem. We developed a protocol, CI-TASSER, to …
(PDB) remains a significant unsolved problem. We developed a protocol, CI-TASSER, to …
Using AlphaFold to predict the impact of single mutations on protein stability and function
MA Pak, KA Markhieva, MS Novikova, DS Petrov… - Plos one, 2023 - journals.plos.org
AlphaFold changed the field of structural biology by achieving three-dimensional (3D)
structure prediction from protein sequence at experimental quality. The astounding success …
structure prediction from protein sequence at experimental quality. The astounding success …
Modeling aspects of the language of life through transfer-learning protein sequences
Background Predicting protein function and structure from sequence is one important
challenge for computational biology. For 26 years, most state-of-the-art approaches …
challenge for computational biology. For 26 years, most state-of-the-art approaches …
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy
W Lee, M Tonelli, JL Markley - Bioinformatics, 2015 - academic.oup.com
SPARKY (Goddard and Kneller, SPARKY 3) remains the most popular software program for
NMR data analysis, despite the fact that development of the package by its originators …
NMR data analysis, despite the fact that development of the package by its originators …
Stimuli-responsive, pentapeptide, nanofiber hydrogel for tissue engineering
Short peptides are uniquely versatile building blocks for self-assembly. Supramolecular
peptide assemblies can be used to construct functional hydrogel biomaterials—an attractive …
peptide assemblies can be used to construct functional hydrogel biomaterials—an attractive …
How fast-folding proteins fold
An outstanding challenge in the field of molecular biology has been to understand the
process by which proteins fold into their characteristic three-dimensional structures. Here …
process by which proteins fold into their characteristic three-dimensional structures. Here …