Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.
J Chem Theory Comput
; 20(14): 6303-6315, 2024 Jul 23.
Article
em En
| MEDLINE
| ID: mdl-38978294
ABSTRACT
Molecular dynamics (MD) simulations are ideally suited to describe conformational ensembles of biomolecules such as proteins and nucleic acids. Microsecond-long simulations are now routine, facilitated by the emergence of graphical processing units. Clustering, which groups objects based on structural similarity, is typically used to process ensembles, leading to different states, their populations, and the identification of representative structures. A popular pipeline combines hierarchical clustering for clustering and selecting the cluster centroid as representative of the cluster. Here, we propose to improve on this approach, by developing a module-Protein Retrieval via Integrative Molecular Ensembles (PRIME), that consists of tools to improve the prediction of the representative in the most populated cluster using extended continuous similarity. PRIME is integrated with our Molecular Dynamics Analysis with N-ary Clustering Ensembles (MDANCE) package and can be used as a postprocessing tool for arbitrary clustering algorithms, compatible with several MD suites. PRIME predictions produced structures that when aligned to the experimental structure were better superposed (lower RMSD). A further benefit of PRIME is its linear scalingârather than the traditional O(N2) traditionally associated with comparisons of elements in a set.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Proteínas
/
Simulação de Dinâmica Molecular
Idioma:
En
Revista:
J Chem Theory Comput
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
Estados Unidos