Prediction
- PleioGRiP 0.02 – Genetic Risk Prediction with Pleiotropy
- BJTEpitope – T-cell Epitope Prediction for the MHC class I allele HLA-A*0201
- Repeatoire – ab inito Prediction of Repeat Families
- growthpred 1.07 – Prediction of Growth-related Traits in Microbes from Genomic and Metagenomic data
- Morpheus 2.0 – Prediction of Transcription Factors Binding Sites based on Position Weight Matrix
- CID-miRNA – miRNA Prediction Webserver
- NetUTR 1.0b – Web server for Prediction of Splice Site in 5′ UTRs
- SFmap 1.7 – Motifs Analysis and Prediction of Splicing Factors
- RNAstructure 5.5 – Prediction & Analysis of RNA Secondary Structure
- Vienna RNA Package 2.1.1 – RNA Secondary Structure Prediction & Comparison
- KNetFold 1.4.4b – RNA secondary structure prediction
- QCS – Quality Control Score For Quality Assessment of Protein Structure Prediction
- NetSurfP 1.0b – Protein Surface Accessibility & Secondary Structure Predictions
- TAPIR 1.1 – Prediction of Plant microRNA Targets
- SCX Prediction Utility 2.2.3994 – Strong Cation Exchange Elution Time Prediction Utility
- Evolving SCFGs 2.0 – RNA Secondary Structure Prediction
- Protemot – Prediction of Protein Binding sites with automatically extracted Geometrical Templates
- MEDock – Web Server for Efficient Prediction of Ligand Binding sites
- PreDNA 1.0 – Accurate Prediction of DNA-binding sites in Proteins
- RAmiRNA – Viral mature MicroRNA prediction Toolkit
- AnaGram – Protein Function Prediction
- PREDIVAC – CD4+ T-cell Epitope Prediction for Vaccine Design
- FREAD 3.0.1 – Database Search Loop Structure Prediction protocol
- BetAware – Beta-Barrel Detection and Topology Prediction
- BayesMendel 2.0-8 – R package for Mendelian Risk Prediction
- CISRR 1.01 – Prediction of Side-chain Modeling
- PCP 1.0 – Protein Complex Prediction
- FSWeight 2.2 – Protein Function Prediction
- SABINE 1.2 – Prediction of the Binding Specificity of Transcription Factors using Support Vector Regression
- FUGUE 20090924 – Protein Structure Prediction using Remote Homology Detection
- PSIVER – Prediction of Protein-protein Interaction Sites in Protein Sequences
- CBS-Pred – Prediction of Carbohydrate-binding sites from Sequence and PSSM
- NETASA – Prediction of Solvent Accessibility using Neural Networks
- RVP-NET 2.0 – Real Value Prediction of Solvent Accessibility
- DBS-PRED – Prediction of DNA-binding in proteins using Neural Networks
- SDCPRED – Specific DNA COntact Prediction
- ProStar – Structural Parameters for Promoter Prediction
- PhoScan – Prediction of Kinase-specific Phosphorylation sites
- FOLD-RATE – Prediction of Protein Folding Rates from Amino Acid Sequence
- DNAbinder – Prediction of DNA-binding Proteins
- SCPRED – Prediction of Stabilization Centers in Proteins
- DNAbind – DNA Binding Protein prediction
- DAS-TMfilter – On filtering False Positive Transmembrane Protein Prediction
- TMBETA-NET – Discrimination and Prediction of Transmembrane Beta Strands in Outer Membrane Proteins
- POODLE – Prediction Of Order and Disorder by machine LEarning
- Pcons – Protein Structure Prediction Meta Server
- metaPPI – Meta Approach for Protein-protein Binding Sites Prediction
- metaPocket 2.0 – Meta approach for Protein Ligand-binding sites Prediction
- SurpResi 201108 – Protein Active Site Prediction based on Central Distances of Amino Acids
- Rahnuma 1.1.1 – Prediction and Analysis of Metabolic Pathways and Comparison of Metabolic Networks
- iPATCH – Prediction of Inter-protein Contact sites
- LOGICOIL – Multi-state Coiled-coil Oligomeric State prediction
- transFold – Super-secondary Structure Prediction of Transmembrane β-barrel proteins
- Reveal – Viewer for Automated active-site Predictions for Polypeptides
- PORTRAIT 1.2 – Prediction of transcriptomic ncRNA by ab initio methods
- PIPS 1.1.2 – Pathogenicity Island Prediction Software
- VitaPred – Prediction of Vitamin Interacting Residues
- VICMpred – Prediction of Functional Proteins of Gram-negative Bacteria using Amino Acid Patterns and Composition
- NTXpred – Prediction of Neurotoxins from their Function and Source
- LGEpred – Correlation Analysis and Prediction of Genes Expression from Amino Acid Sequence of Proteins
- SRTpred – SVM based method for Prediction of Secrteory Proteins
- BTXpred – Prediction of Bacterial Toxins
- MANGO – Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)
- GPCRpred – Prediction of Families & Superfamilies of G-protein Coupled receptors
- NRpred – SVM based method for Prediction of Nuclear Receptors
- MHC2Pred – SVM based method for MHC class II Binders Prediction
- HLADR4Pred – SVM and ANN based HLA-DR Bininding Peptide Prediction
- SARpred – Prediction of real value of Surface Accessibility in proteins from Amino Acid Sequence
- BhairPred – Prediction of beta Hairpins in Proteins using ANN and SVM Techniques
- PEPstr – Peptide Tertiary Structure Prediction
- Betaturns – Prediction of Beta-turn Types
- TBBpred – Transmembrane Beta Barrel prediction
- Ar_NHPred – Prediction of Aromatic Backbone NH Interaction in Proteins
- AlphaPred – Prediction of Alpha-turns in Proteins using Multiple Alignment and Secondary Structure Information
- GammaPred – Prediction of Gamma-turns in Proteins using Multiple Alignment and Secondary Structure Information
- BetaTPred2: Prediction of Beta-turns in Proteins using Neural Networks and Multiple Alignment
- BTEVAL – Evaluation of beta-turn Prediction
- APSSP2 – Advanced Protein Secondary Structure Prediction Server
- GenemiR 1.0 – Unified Search of Mammalian microRNA Target Predictions
- GolgiP – Prediction of Plant Golgi Proteins
- BSPP – Blood Secreted Protein Prediction
- XtalPred – Prediction of Protein Crystallizability
- MinPath 1.2 – Biological Pathway Reconstructions using Protein Family Predictions
- SLocX - Prediction of Protein subcellular localization using Gene Expression
- NAbind – RNA Binding Prediction Package
- Phos3D – Prediction of Phosphorylation Sites (P-sites) in Proteins
- TargetScan 6.2 – Prediction of microRNA Targets
- GenomeScan 1.0 – Prediction of Gene Structures in Genomic Sequences
- ACEScan 1.0 – Prediction of Conserved Alternatively Spliced Exons from pairs of Conserved Mouse/Human Exons
- TSEMA – Prediction of Protein Pairings between interacting families
- LIPO – Prediction of Lipo-boxes in Gram-negative bacterial Protein Sequences
- RetroPred – Prediction, Classification and Extraction of non-LTR Retrotransposons
- TpPred – Prediction and Classification of Transport proteins
- PAGODA – Gene Function Prediction in Plasmodium Falciparum
- GO-At – Gene Function Prediction in Arabidopsis Thaliana
- Q-SiteFinder – Ligand Binding Site Prediction
- EpiGRAPH 1.0 – Statistical Analysis and Prediction of Epigenomic data
- snoGPS 1.0 – H/ACA snoRNA predictions
- Snoscan 1.0 – C/D box snoRNA Predictions
- TraceGD 1.0 – Genetic Disease Prediction tool
- FindtRNA 1.0 – tRNA Prediction tool
- SeqRate 1.0 – Sequence-based Prediction of Protein Folding rates
- PSSpred v2 – Multiple Neural Network Training program for Protein Secondary Strucure Prediction
- Metadisorder – Prediction of Intrinsically Unstructured Proteins (protein disorder) from Amino Acid Sequence only
- GeneMANIA 3.1 – Gene Function Prediction
- NRProF – Protein Function Prediction Based on the Neural Response Algorithm
- SSpro / ACCpro 4.1 – Protein Secondary Structure /Solvent Accessibility Prediction with Homology Analysis
- SVMcon 1.0 – Protein Contact Map Prediction using Support Vector Machine
- NNcon 1.0 – Protein Contact Map Prediction Using Artificial Neural Networks
- InterPreTS – Interaction Prediction through Tertiary Structure
- TargetPrediction – Target mRNAs Prediction
- TargetMiner – microRNA Target Prediction
- RNAwolf 0.3.2 / MC-Fold-DP – RNA Secondary Structure Prediction.
- miRFinder 4.0 – MicroRNA Prediction
- HLAminer 1.0.5 – Derivation of HLA class I Predictions from Shotgun sequence datasets
- GPS-ARM 1.0 – Prediction of D-boxes and KEN-boxes
- GPS-PUP 1.0 – Prediction of Pupylation Sites
- GPS-Polo 1.0 – Prediction for Polo-like kinases
- GPS-YNO2 1.0 – Prediction of Tyrosine Nitration Sites
- GPS-SNO 1.0 – S-nitrosylation Sites Prediction
- iGPS 1.0.1 – Prediction of Site-specific Kinase-substrate Relations from Phosphoproteomic data
- CSS-Palm 3.0 – Palmitoylation Site Prediction with a Clustering and Scoring Strategy
- SSP 1.0 – SUMO Substrates Prediction
- SUMOsp 2.0.4 – SUMOylation sites Prediction
- GPS 2.1.2 – Kinase-specific Phosphorylation Site Prediction
- DEEP 1.0.3 – Differential Expression Effector Prediction
- SHIFTX2 1.07 – Improved Protein Chemical Shift Prediction
- LocTree2 – Protein Sub-cellular Localization Prediction for all domains of life
- PRNA – Prediction of protein-RNA binding sites
- SymmDock Beta 1.0 – Prediction of Complexes with Cn Symmetry
- GOAP – Protein Structure Prediction
- HHMMiR 1.2 – Prediction of microRNAs using Hierarchical Hidden Markov models
- Prediction of Protein-DNA Interactions based on Alpha Shape Modeling
- PSIPRED 3.3 – Accurate Protein Secondary Structure Prediction
- PAM 2.1 – Prediction and Survival Analysis for Genomic Expression Data Mining
- MultiTF-PPI – Competitive Transcription Factor Binding Prediction
- 2ZIP – Prediction of Leucine Zipper Domain from the Protein Sequence
- TMpred 1.0 – Prediction of Transmembrane Regions and Orientation
- COILS 2.2 – Prediction of Coiled Coil Regions in Proteins
- SI-FI 3.1 – RNAi (RNA interference) Off-target Prediction
- GAPIT – Genome Association and Prediction Integrated Tool
- miRComp – Composite MicroRNA Target Prediction
- POLYPHEN 2.2.2 – Prediction of Functional Effects of Human nsSNPs
- Strut 0.1 – Protein Function Prediction
- Nucleosomes Positioning 3.0 – Prediction by Genomic Sequence
- GAMES 1.3 – Prediction of Functional Effect of Mutation
- PASTA 1.0 – Protein Aggregation Prediction
- KLR – Integrated Protein Function Prediction
- CROP 1.33 – Clustering 16S rRNA For OTU Prediction
- SIDEpro 1.0 – Prediction of Protein side-chain Conformations
- SOLpro – Prediction of Protein Solubility upon Overexpression
- SELECTpro 1.0 – Protein Model Scoring/Selection and Side-Chain Prediction
- DISpro 1.0 – Prediction of Disordered Regions from Protein Sequences
- DIpro 2.0 – Protein Disulfide Bond Prediction
- DOMpro 1.0 – Protein Domain Prediction
- MUpro 1.1 – Prediction of Protein Stability Changes for Single Site Mutations from Sequences
- ProteinEvaluator 1.0.0 – Protein Sequence Prediction Evaluator
- MAGprediction – Gene Allele Prediction Using Unphased SNP data
- JPOP 0.1 – Prediction of Operon Structures
- Cubic 2.0.4 / JCubic 1.1 – Protein Binding Site Prediction
- Musite 1.0.1 – Prediction of Both General and Kinase-specific Protein Phosphorylation Sites
- MUPRED – Protein Secondary Structure Prediction
- GeneFAS – Gene Function Prediction
- Bhageerath 1.0 – Energy Based Protein Structure Prediction
- SymCurv 2.0 – Predictions of Nucleosome Positions for a Given Sequence
- PKNOTS 1.07 – RNA Pseudoknot Prediction
- Isofinder – Isochore Computational Prediction
- FunSiP 0.8.1b – Prediction of Functional Sites in DNA
- TRAP 3.04 – Transcription factor Affinity Prediction
- Orb 1.2 / orbplus 1.1.2 – Chemical Shift Prediction
- GOtcha 200812 – Prediction of Gene Function by Application of Gene Ontology
- Twinscan/N-SCAN 4.1.2 – Gene Structure Prediction
- Kinwalker – Algorithm for Prediction of RNA Folding Trajectories
- AveRNA – Ensemble-based Prediction of RNA Secondary Structures.
- SPuNC – RNA Structure Prediction using Nucleotide Composition
- SVMSEQ 1.0 – Protein Contact Prediction
- I-TASSER 1.1 – Protein Structure & Function Predictions
- DisEMBL 1.5 – Protein Disorder Prediction
- InteroPorc 2.0.2 – Automatic Molecular Interaction Predictions
- NOXclass – Prediction of Protein-protein Interaction Types
- MEMPACK – SVM Prediction of Membrane Helix Packing
- DISOPRED 2.43 – Intrinsic Protein Disorder Prediction
- TESTLoc – Protein Localization Prediction based on ESTs
- CONTRAfold 2.02 – RNA Secondary Structure Prediction
- CDPred 1.01 – Conserved Domain-based Prediction
- ProCope 1.2 – Protein Complex Prediction and Evaluation
- MeltDNA 1.0.1 – DNA Hybridization & Melting Thermodynamics Prediction
- Rnall 2.0 – RNA Local Secondary Structure Prediction
- HMMSTR-CM – Protein Contact Map Prediction
- HMMSTR 20091212 – Protein Secondary Structure Prediction
- SecretomeP 2.0 – Prediction of Non-classical Protein Secretion
- LipoP 1.0a – Prediction of Lipoproteins & Signal Peptides in Gram Negative Bacteria
- EasyGene 1.2c – Prediction of Genes in Prokaryotes
- assp 1.2 – Assess Protein Secondary Structure Prediction Accuracy
- EMMA 1.1 – Prediction & Alignment of Cis-regulatory Modules
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