Genomics/Proteomics

• Biological General Repository for Interaction Datasets: is an interaction repository with data compiled through comprehensive curation efforts. All data are freely provided via search index and available for download in standardized formats.
• STRING Protein-Protein interaction networks
• Human Protein Reference Database 
• Structural Genomic Portal
• IntAct: EBI’s interaction database from the literature
• Genomes Online Database: GOLD
• Lipidomics
• ENCODE: international collaboration of research groups, goal is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.
• PPI: Protein-Protein interaction resources 

Graphics & Modeling

• Pymol Wiki
• Morphing movies in Pymol with a Mac
• Weizmann Institute extensive list of protein-protein docking options
• Modeller: comparative protein structure
• WHATIF: molecular modeling and drug design
• ClusPro: protein/protein interactions, uses PDB input
• LigPlot+ : multiple ligand-protein interaction diagrams
• PsiPred: Protein structure prediction from sequence – can run jobs on the server or download software

Sequence Evaluation and Comparison

• ExPASy Bioinformatics: calculate a theoretical MW or pI, perform a sequence alignment, predict cleavage sites, and much more
• EMBL-EBI Services: European Bioinformatics Institute, capable of DNA, protein multiple sequence alignments
• NCBI RefSeq: A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein
• NCBI BLAST
• MATTFash: multiple sequence alignments
• SEEKQUENCHER: pulls sequences from databanks
• EMBOSS: suite of bioinformatic tools
• ESPript 3: pretty sequence alignments for publications, lots of colors
• SMART: Simple Modular Architecture Research Tool
• Disulfide by Design: application for the rational design of disulfide bonds in proteins. For a given protein structural model, all residue pairs are rapidly assessed for proximity and geometry consistent with disulfide formation – assuming the residues were mutated to cysteines
• HMMER: biosequence analysis using profile hidden Markov models

Structural Evaluation and Comparison

• List of Surface and Volume Programs
• Protein Data Bank: data base for 3-D structures of proteins
• Phobius: transmembrane topology and signal peptide predictor, FASTA input
• Naccess: calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessibilities for both proteins and nucleic acids.
• Protein Interaction Server : surface calculations
• Monster:  non-covalant interactions in proteins
• VADAR: Volume, Area, Dihedral Angle Reporter
• PARVATI: anisotropic displacement parameters statistics
• CASTp: identification and measurements of surface accessible pockets as well as interior inaccessible cavities
• BBCU binding site prediction and docking 
• Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis
• FATCAT: structure alignment is formulated as the AFPs (aligned fragment pairs) chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0.
• SCOPe: Structural Classification of Proteins
• SiteEngine: functional site search engine; recognizes regions on the surface of one protein that resemble a specific binding site of another
• POSA (Partial Order Structure Alignment): A flexible multiple structure alignment approach