Treat cancers by targeting survivin: just a dream or future reality?
Since the discovery of survivin (BIRC5) as a cancer-related molecule by Grazia Ambrosini
and Dario C. Altieri at 1997, our knowledge related to the function of this molecule has been …
and Dario C. Altieri at 1997, our knowledge related to the function of this molecule has been …
Computational approaches to RNA structure prediction, analysis, and design
C Laing, T Schlick - Current opinion in structural biology, 2011 - Elsevier
RNA molecules are important cellular components involved in many fundamental biological
processes. Understanding the mechanisms behind their functions requires RNA tertiary …
processes. Understanding the mechanisms behind their functions requires RNA tertiary …
Capturing RNA folding free energy with coarse-grained molecular dynamics simulations
We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER
(RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number …
(RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number …
Protein folding prediction in the HP model using ions motion optimization with a greedy algorithm
Background The function of a protein is determined by its native protein structure. Among
many protein prediction methods, the Hydrophobic-Polar (HP) model, an ab initio method …
many protein prediction methods, the Hydrophobic-Polar (HP) model, an ab initio method …
An effective hybrid of hill climbing and genetic algorithm for 2D triangular protein structure prediction
Background Proteins play fundamental and crucial roles in nearly all biological processes,
such as, enzymatic catalysis, signaling transduction, DNA and RNA synthesis, and …
such as, enzymatic catalysis, signaling transduction, DNA and RNA synthesis, and …
[HTML][HTML] Network theory tools for RNA modeling
An introduction into the usage of graph or network theory tools for the study of RNA
molecules is presented. By using vertices and edges to define RNA secondary structures as …
molecules is presented. By using vertices and edges to define RNA secondary structures as …
GARN: Sampling RNA 3D structure space with game theory and knowledge-based scoring strategies
Cellular processes involve large numbers of RNA molecules. The functions of these RNA
molecules and their binding to molecular machines are highly dependent on their 3D …
molecules and their binding to molecular machines are highly dependent on their 3D …
On the characterization and software implementation of general protein lattice models
A Bechini - PloS one, 2013 - journals.plos.org
Abstract models of proteins have been widely used as a practical means to computationally
investigate general properties of the system. In lattice models any sterically feasible …
investigate general properties of the system. In lattice models any sterically feasible …
AutoRNA: RNA tertiary structure prediction using variational autoencoder
MA Kazanskii, L Uroshlev, F Zatylkin, I Pospelova… - bioRxiv, 2024 - biorxiv.org
Understanding the RNA tertiary structure is crucial for advancing therapeutic development
and vaccine design. Previous methods, such as dynamic simulations, have been used to …
and vaccine design. Previous methods, such as dynamic simulations, have been used to …
A conditional random fields method for RNA sequence–structure relationship modeling and conformation sampling
Accurate tertiary structures are very important for the functional study of non-coding RNA
molecules. However, predicting RNA tertiary structures is extremely challenging, because of …
molecules. However, predicting RNA tertiary structures is extremely challenging, because of …