Resources

UMass Amherst

• About Amherst: official website
• Directions to UMass Amherst Campus
• Chemistry-Biology Interface Program (CBI)
• Molecular & Cellular Biology Program (MCB)
• UMass Amherst Library Databases & Collections
• UMass Amherst Information Technology
• UMass Amherst Environmental Health & Safety Fact Sheets
• Chemistry Computer Resource Center
• Chemistry Booking System

Journals

• Science
• Nature
• Nature Biotechnology
• Nature Nanotechnology
• Nature Chemistry
• Nature Methods
• Nature Chemical Biology
• Nature Communications
• Journal of the American Chemical Society
• Angewandte Chemie International Edition

Softwares and Servers

• NUPACK: analysis and design of nucleic acid structures
• mFold & UNAFold: nucleic acid folding and hybridization prediction
• LocARNA: RNA alignment and folding
• OligoCalc: DNA/RNA properties calculator
• KineFold: animating RNA folding
• caDNAno: DNA origami design program
• CanDo: predicting 3D shape and flexibility of programmed DNA assembly
• DAEDALUS: DNA origami sequence design algorithm for user-defined structures
• NanoTiler: design of RNA nanostructure
• RNA2D3D: convert RNA 2D structures to 3D modeling
• SnapGene: plasmid map editor
• ApE: another plasmid map editor
• EteRNA: a browser-based game to solve puzzles about RNA folding
• sciNote: free open source electronic lab notebook

Database and Protocols

• Nucleic Acid Database: experimentally-determined 3D nucleic acids and complex assemblies
• RNAJunction: database for RNA junction and kissing loop
• Rfam: RNA families database
• Bionumbers: database of useful biological numbers
• Benchfly: science video platform with many useful protocols and techniqeus
• JoVE: Journal of Visualized Experiments, with movies for many detailed protocols and techniques
• Protocol Online: protocols and forum discussion
• NEB Tools & Resources: New England Biolabs