Chemical Structural Similarity Analysis
Cut a Tree into Groups of Data
Chemical dissimilarity.
Detection of clusters.
Metabolite-associated Diseases
Metabolite-associated Enzymes
Cluster features extraction
KODAMA chemical similarity.
Name of metabolites
Metabolic Pathways
Physical Proprieties of metabolites
Metabolite Cards Reading
Metabolites selection
Metabolite substituents
Metabolite Taxonomy
Optimal cluster number calculation.
Weighted Metabolite Chemical Structural Analysis
Write a CLS file
Write a GCT file
Write a GMT file
A new pipeline to explore chemical structural similarity across metabolites. It allows the metabolite classification in structurally-related modules and identifies common shared functional groups. The KODAMA algorithm is used to highlight structural similarity between metabolites. See Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA. (2017) Bioinformatics <doi:10.1093/bioinformatics/btw705>, Cacciatore S, Luchinat C, Tenori L. (2014) Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>, and Abdel-Shafy EA, Melak T, MacIntyre DA, Zadra G, Zerbini LF, Piazza S, Cacciatore S. (2023) Bioinformatics Advances <doi:10.1093/bioadv/vbad053>.