• AutoDock

  • Referenced in 34 articles [sw09659]
  • designed to predict how small molecules, such as substrates or drug candidates, bind...
  • DrugBank

  • Referenced in 30 articles [sw23876]
  • contains 60% more FDA-approved small molecule and biotech drugs including 10% more ‘experimental’ drugs...
  • COSMOS

  • Referenced in 8 articles [sw04049]
  • COSMOS (COmparing Small MOlecules for Similarity) is a computer program to compare (small) molecules...
  • Pathway Commons

  • Referenced in 9 articles [sw23072]
  • physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathway Commons aims to collect...
  • HMDB

  • Referenced in 9 articles [sw28995]
  • electronic database containing detailed information about small molecule metabolites found in the human body...
  • PubChem

  • Referenced in 5 articles [sw23142]
  • PubChem: Integrated Platform of Small Molecules and Biological Activities. PubChem is an open repository ... data identifying the biological activities of small molecules. PubChem contents include more than: 1000 bioassays ... mining the biological information of small molecules...
  • iPfam

  • Referenced in 8 articles [sw29349]
  • include interaction data for domain bound small molecule ligands. Functional annotations are provided from source...
  • 2L-piRNA

  • Referenced in 25 articles [sw27667]
  • length. Given a small non-coding RNA molecule, can we predict whether...
  • BindingDB

  • Referenced in 7 articles [sw23141]
  • mutational variants, and approximately 11,000 small molecule ligands. The data are extracted from...
  • ChemmineR

  • Referenced in 4 articles [sw33261]
  • cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains...
  • SYBYL

  • Referenced in 4 articles [sw14073]
  • comprehensive tools for molecular modeling— including small molecule and macromolecular modeling and simulation, cheminformatics, lead...
  • PatchDock

  • Referenced in 4 articles [sw27636]
  • prediction of protein–protein and protein–small molecule complexes. The SymmDock method predicts the structure...
  • MOLDEN

  • Referenced in 4 articles [sw20678]
  • combined Amber (protein) and GAFF (small molecules) force fields. Atom typing can be done automatically...
  • SMPDB

  • Referenced in 2 articles [sw29378]
  • SMPDB (The Small Molecule Pathway Database) is an interactive, visual database containing more than ... small molecule pathways found in humans only. The majority of these pathways are not found ... protein_complex quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained...
  • Screensaver

  • Referenced in 2 articles [sw21449]
  • common in academe as large-scale small molecule and genome-scale RNAi screening strategies ... address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports ... genome-scale RNAi screening projects and small molecule screening projects. Conclusions: The informatics and administrative...
  • MolAxis

  • Referenced in 3 articles [sw35343]
  • that represent probable routes taken by small molecules passing through channels. The outer medial axis...
  • cctbx

  • Referenced in 3 articles [sw15298]
  • cctbx is therefore also useful for small-molecule crystallography and even general scientific applications...
  • SpectralNET

  • Referenced in 3 articles [sw26161]
  • chemical genetics. Networks of genes, proteins, small molecules, or other objects of study...
  • SM2miR

  • Referenced in 1 article [sw29357]
  • database of the experimentally validated small molecules’ effects on microRNA expression. The inappropriate expression ... many studies have demonstrated that bioactive small molecules (or drugs) can regulate miRNA expression, which ... indicates that targeting miRNAs with small molecules is a new therapy for human diseases ... which recorded 2925 relationships between 151 small molecules and 747 miRNAs in 17 species after...
  • iMiRNA-PseDPC

  • Referenced in 10 articles [sw22425]
  • microRNA (miRNA) is a small non-coding RNA molecule, functioning in transcriptional and post-transcriptional...