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 …
[HTML][HTML] Adaptability and specificity: how do proteins balance opposing needs to achieve function?
Many proteins select from a small repertoire of 3-dimensional folds retained over evolutional
timescales and recruited for different functions, with changes in local structure and sequence …
timescales and recruited for different functions, with changes in local structure and sequence …
The impact of AlphaFold2 on experimental structure solution
AlphaFold2 is a machine-learning based program that predicts a protein structure based on
the amino acid sequence. In this article, we report on the current usages of this new tool and …
the amino acid sequence. In this article, we report on the current usages of this new tool and …
Revealing Missing Protein–Ligand Interactions Using AlphaFold Predictions
N Escobedo, T Saldaño, J Mac Donagh… - Journal of Molecular …, 2024 - Elsevier
Protein–ligand interactions represent an essential step to understand the bases of molecular
recognition, an intense field of research in many scientific areas. Structural biology has …
recognition, an intense field of research in many scientific areas. Structural biology has …
[HTML][HTML] “Protein” no longer means what it used to
Every biologist knows that the word protein describes a group of macromolecules essential
to sustain life on Earth. As biologists, we are invariably trained under a protein paradigm …
to sustain life on Earth. As biologists, we are invariably trained under a protein paradigm …
Homology modeling in a dynamical world
A key concept in template‐based modeling (TBM) is the high correlation between sequence
and structural divergence, with the practical consequence that homologous proteins that are …
and structural divergence, with the practical consequence that homologous proteins that are …
Protein structure, dynamics and assembly: Implications for drug discovery
Most of the therapeutic drugs available in the market today, are targeted against proteins.
Drug molecules are designed to complement shape, size and electrostatic fingerprints of the …
Drug molecules are designed to complement shape, size and electrostatic fingerprints of the …
Ghost interactions: revealing missing protein-ligand interactions using AlphaFold predictions
Protein–ligand interactions represent an essential step in understanding molecular
recognition, an intense field of research for many scientific areas. Structural biology has …
recognition, an intense field of research for many scientific areas. Structural biology has …
How is structural divergence related to evolutionary information?
The analysis of evolutionary information in a protein family, such as conservation and
covariation, is often linked to its structural information. Multiple sequence alignments of …
covariation, is often linked to its structural information. Multiple sequence alignments of …
Ensembles from ordered and disordered proteins reveal similar structural constraints during evolution
The conformations accessible to proteins are determined by the inter-residue interactions
between amino acid residues. During evolution, structural constraints that are required for …
between amino acid residues. During evolution, structural constraints that are required for …