Protein ensembles link genotype to phenotype
R Nussinov, CJ Tsai, H Jang - PLoS computational biology, 2019 - journals.plos.org
Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical
studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype …
studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype …
Impact of protein conformational diversity on AlphaFold predictions
T Saldaño, N Escobedo, J Marchetti, DJ Zea… - …, 2022 - academic.oup.com
Motivation After the outstanding breakthrough of AlphaFold in predicting protein 3D models,
new questions appeared and remain unanswered. The ensemble nature of proteins, for …
new questions appeared and remain unanswered. The ensemble nature of proteins, for …
Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications
Proteins are dynamical entities that undergo a plethora of conformational changes,
accomplishing their biological functions. Molecular dynamics simulation and normal mode …
accomplishing their biological functions. Molecular dynamics simulation and normal mode …
[图书][B] Introduction to proteins: structure, function, and motion
Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the
structure, function, and motion of proteins for students, faculty, and researchers at all levels …
structure, function, and motion of proteins for students, faculty, and researchers at all levels …
CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state
CoDNaS (conformational diversity of the native state) is a protein conformational diversity
database. Conformational diversity describes structural differences between conformers that …
database. Conformational diversity describes structural differences between conformers that …
Selection on protein structure, interaction, and sequence
PB Chi, DA Liberles - Protein Science, 2016 - Wiley Online Library
Characterizing the probabilities of observing amino acid substitutions at specific sites in a
protein over evolutionary time is a major goal in the field of molecular evolution. While purely …
protein over evolutionary time is a major goal in the field of molecular evolution. While purely …
Conformational diversity analysis reveals three functional mechanisms in proteins
Protein motions are a key feature to understand biological function. Recently, a large-scale
analysis of protein conformational diversity showed a positively skewed distribution with a …
analysis of protein conformational diversity showed a positively skewed distribution with a …
Efficient conversion of acids and esters to amides and transamidation of primary amides using OSU-6
Abstract OSU-6, an MCM-41 type hexagonal mesoporous silica with strong Bronsted acid
properties, has been used to promote the high-yield conversion of carboxylic acids and …
properties, has been used to promote the high-yield conversion of carboxylic acids and …
Evolutionary conserved positions define protein conformational diversity
Conformational diversity of the native state plays a central role in modulating protein
function. The selection paradigm sustains that different ligands shift the conformational …
function. The selection paradigm sustains that different ligands shift the conformational …
In proteins, the structural responses of a position to mutation rely on the Goldilocks principle: not too many links, not too few
R Dorantes-Gilardi, L Bourgeat, L Pacini… - Physical Chemistry …, 2018 - pubs.rsc.org
A disease has distinct genetic and molecular hallmarks such as sequence variants that are
likely to produce the alternative protein structures accountable for individual responses to …
likely to produce the alternative protein structures accountable for individual responses to …