Recent advances in the improvement of enzyme thermostability by structure modification

Z Xu, YK Cen, SP Zou, YP Xue… - Critical reviews in …, 2020 - Taylor & Francis
Thermostability is considered to be an important parameter to measure the feasibility of
enzymes for industrial applications. Generally, higher thermostability makes an enzyme …

Rational engineering of enzyme stability

VGH Eijsink, A Bjørk, S Gåseidnes, R Sirevåg… - Journal of …, 2004 - Elsevier
During the past 15 years there has been a continuous flow of reports describing proteins
stabilized by the introduction of mutations. These reports span a period from pioneering …

[PDF][PDF] The PDB_REDO server for macromolecular structure model optimization

RP Joosten, F Long, GN Murshudov, A Perrakis - IUCrJ, 2014 - journals.iucr.org
The refinement and validation of a crystallographic structure model is the last step before the
coordinates and the associated data are submitted to the Protein Data Bank (PDB). The …

Comparative protein structure modeling using MODELLER

B Webb, A Sali - Current protocols in bioinformatics, 2016 - Wiley Online Library
Comparative protein structure modeling predicts the three‐dimensional structure of a given
protein sequence (target) based primarily on its alignment to one or more proteins of known …

An end-to-end deep learning method for protein side-chain packing and inverse folding

M McPartlon, J Xu - … of the National Academy of Sciences, 2023 - National Acad Sciences
Protein side-chain packing (PSCP), the task of determining amino acid side-chain
conformations given only backbone atom positions, has important applications to protein …

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

R Guerois, JE Nielsen, L Serrano - Journal of molecular biology, 2002 - Elsevier
We have developed a computer algorithm, FOLDEF (for FOLD-X energy function), to provide
a fast and quantitative estimation of the importance of the interactions contributing to the …

Bayesian statistical analysis of protein side‐chain rotamer preferences

RL Dunbrack Jr, FE Cohen - Protein science, 1997 - Wiley Online Library
We present a Bayesian statistical analysis of the conformations of side chains in proteins
from the Protein Data Bank. This is an extension of the backbone‐dependent rotamer library …

Heterozygous germline mutations in the p53 homolog p63 are the cause of EEC syndrome

J Celli, P Duijf, BCJ Hamel, M Bamshad, B Kramer… - Cell, 1999 - cell.com
EEC syndrome is an autosomal dominant disorder characterized by ectrodactyly,
ectodermal dysplasia, and facial clefts. We have mapped the genetic defect in several EEC …

Assessing protein structures with a non-local atomic interaction energy

F Melo, E Feytmans - Journal of molecular biology, 1998 - Elsevier
We describe a new approach, based on the energy of non-local interactions, to assess
protein structures. The method uses a very sensitive and accurate atomic mean force …

Diffpack: A torsional diffusion model for autoregressive protein side-chain packing

Y Zhang, Z Zhang, B Zhong… - Advances in Neural …, 2024 - proceedings.neurips.cc
Proteins play a critical role in carrying out biological functions, and their 3D structures are
essential in determining their functions. Accurately predicting the conformation of protein …