The interface of protein structure, protein biophysics, and molecular evolution
Abstract The interface of protein structural biology, protein biophysics, molecular evolution,
and molecular population genetics forms the foundations for a mechanistic understanding of …
and molecular population genetics forms the foundations for a mechanistic understanding of …
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations
Understanding how a mutation might affect protein stability is of significant importance to
protein engineering and for understanding protein evolution genetic diseases. While a …
protein engineering and for understanding protein evolution genetic diseases. While a …
Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset
Predicting the difference in thermodynamic stability between protein variants is crucial for
protein design and understanding the genotype-phenotype relationships. So far, several …
protein design and understanding the genotype-phenotype relationships. So far, several …
INPS-MD: a web server to predict stability of protein variants from sequence and structure
Motivation: Protein function depends on its structural stability. The effects of single point
variations on protein stability can elucidate the molecular mechanisms of human diseases …
variations on protein stability can elucidate the molecular mechanisms of human diseases …
Reductive genome evolution in Buchnera aphidicola
RCHJ Van Ham, J Kamerbeek… - Proceedings of the …, 2003 - National Acad Sciences
We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the
aphid Baizongia pistacea. This strain diverged 80–150 million years ago from the common …
aphid Baizongia pistacea. This strain diverged 80–150 million years ago from the common …
DDGun: an untrained predictor of protein stability changes upon amino acid variants
L Montanucci, E Capriotti, G Birolo… - Nucleic Acids …, 2022 - academic.oup.com
Estimating the functional effect of single amino acid variants in proteins is fundamental for
predicting the change in the thermodynamic stability, measured as the difference in the …
predicting the change in the thermodynamic stability, measured as the difference in the …
DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations
L Montanucci, E Capriotti, Y Frank, N Ben-Tal… - BMC …, 2019 - Springer
Background Predicting the effect of single point variations on protein stability constitutes a
crucial step toward understanding the relationship between protein structure and function …
crucial step toward understanding the relationship between protein structure and function …
An antisymmetric neural network to predict free energy changes in protein variants
The prediction of free energy changes upon protein residue variations is an important
application in biophysics and biomedicine. Several methods have been developed to …
application in biophysics and biomedicine. Several methods have been developed to …
Role of water mediated interactions in protein− protein recognition landscapes
GA Papoian, J Ulander… - Journal of the American …, 2003 - ACS Publications
The energy landscape picture of protein folding and binding is employed to optimize a
number of pair potentials for direct and water-mediated interactions in protein complex …
number of pair potentials for direct and water-mediated interactions in protein complex …
Extending the PRIME model for protein aggregation to all 20 amino acids
We extend PRIME, an intermediate‐resolution protein model previously used in simulations
of the aggregation of polyalanine and polyglutamine, to the description of the geometry and …
of the aggregation of polyalanine and polyglutamine, to the description of the geometry and …