|| Short Description
|| Prominent Examples
| Protein Structure Prediction
|| pAb initio protein structure prediction software
|| This type of software builds 3D protein models based on physical principles, not previously solved structure.
|| Structures are predicted via protein folding mimicry or stochastic methods and complements structural bioinformatics and structural genomics fields.
|| Selvita Protein Modeling Platform, ROBETTA, Abalone
|| pAb initio software often requires enormous computational resources to predict structure, and therefore it is only used for tiny proteins.
| Comparative protein structure modeling software
|| This type of software uses previously solved structures as starting points (or templates) for protein structure prediction. Comparative protein structure modeling can be split into two groups: homology modeling and protein threading.
|| Comparative protein structure software does not require as much computing power because its search space is narrower.
|| SWISS-MODEL, ESyPred3D, MODELLER
|| Often get error in comparative protein structure modeling because of poor template selection and inaccuracies in target-template sequence alignment.
| Gene Function
|| Controlled vocabularies for gene/enzyme function
|| Controlled vocabularies organize knowledge for subsequent retrieval. EC number (Enzyme Commision Number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. Gene Ontology is an initiative to organize gene products into categories
|| Use these vocabularies to search for genes or enzymes of a specific function and easily find related material. Remove some ambiguities in termonology.
|| EC Numbers, Gene Ontology, UniProt
| Biochemical pathway databases
|| Databases of metabolic pathways stored as processes broken down into molecular events. Databases tend to be made for pathways from specific model organism (ie- humans, ecoli, mice).
|| Search for involvement of specific molecules or processes across pathways.
|| Reactome, EcoCyc, MouseCyc
|| Need a standardized ontology of terms describe the subcellular locations of molecules and reactions, molecular functions, and the larger biological processes that a specific reaction is part of
| Structure Analysis
|| Protein/protein docking software
|| Software that predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex.*
|| Knowledge of the preferred orientation can be used to predict the binding affinity between two molecules.
|| FTDock, FADE and PADRE,
|| Ligand and protein are not rigid and can adjust their conformation during binding to create a “best-fit” and and this can be difficult to predict/model.
| Protein/small-molecule docking software
|| Models protein/small ligand complexes.
|| Useful in drug design.
|| AutoDock, ROSETTALIGAND
| Sequence Analysis
|| Sequence Assembly Software
|| Sequence assembly software is used to align and merge fragments of long DNA sequences in order to reconstruct original sequences.
|| This type of software is useful for initiatives like the Human Genome project because DNA sequencing technology cannot read whole genomes all at once. It is read in smaller pieces (between 20 and 1000 bases) and assembled to form a complete genome sequence.
|| AMOS, ABySS, Phrap, TIGR Assembler
|| Genomes are extremely long and it takes an enormous amount of assembling to make sequencing reads into a complete genome.
| Gene-finding Software
|| Gene finding software algorithmically identifies stretches of sequence, usually genomic DNA, that are biologically functional.
|| The next step after sequencing is gene finding in order to begin to characterize a genome.
|| GenMark, BLAST
| RNA Structure
|| RNA folding software
|| RNA folding software predicts 3D RNA structure by analyzing secondary structure (which usually provides a scaffold for 3D structure). Similar to protein structure prediction software: ab initio or comparative.
|| Can use RNA folding software to predict function.
|| MASTR, R-COFFEE, Sfold
|| RNA structure prediction software usually excludes the pseudoknot (certain type of secondary RNA structure).
| RNA design software
|| RNA design software is used to design RNA complexes with specific structure and functions.
|| Create RNAi for specific gene-knockout research
|| RNAsoft, Sfold
Proteins. 2006 Nov 15;65(3):538-48.