Protein Sequence Analysis
- PocketMatch 2.0 – Compare a pair of Binding Sites
- Matcher – Analyze whether Sequence contains Repeated Pattern
- Entropy Calculator 3.3.1 – Multiple Sequence Alignment Scoring
- PROVEAN 1.1.3 – Protein Variation Effect Analyzer
- BJTEpitope – T-cell Epitope Prediction for the MHC class I allele HLA-A*0201
- PFP 2.2 – Extracting and Displaying Positive Electrostatic Patches on Protein Surfaces
- ProtViz 0.1.47 – Proteomics Data Analysis & Visualization
- SequenceAssembly 20111004 – Assemble Amino Acid Sequences of Entire Proteins
- SequenceAssignCompare 20111109 – Automated MALDI-ISD Protein Sequencing Software
- DBToolkit 4.2 – Manipulating fasta Sequence Databases
- Thermo MSF Parser 2.0.2 – Parser and Viewer for Thermo msf files
- PeptideShaker 0.19.3 – Interpretation of Proteomics Identifications from multiple search engines
- OMSSA Parser 1.5.9 – Java based Parser for OMSSA omx files
- FragmentationAnalyzer 1.5.9 – Analyze MS/MS Fragmentation Data
- SearchGUI 1.12.2 – GUI for Proteomics Identification Search Engines
- Compomics-utilities 3.11.27 – Java Library encompassing shared code of various Proteomics research projects
- DSSP 2.1.0 – Calculates DSSP Entries from PDB Entries
- PatternLab for proteomics 2.2.0.1 – tool for analyzing Shotgun Proteomic data
- TM-score 20121217 – Calculate Similarity of Topologies of two Protein Structures
- SHARPEN 1.5.1 – Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network
- MESSA – MEta Server for Protein Sequence Analysis
- QCS – Quality Control Score For Quality Assessment of Protein Structure Prediction
- Seq2Ref V1 beta – Facilitate Functional Interpretation
- ProteoWizard 3.0.4472 – Proteomics Data Analysis
- OSPREY 2.1 – Computational Structure-based Protein Design
- PISCES 20130411 – Protein Sequence Culling Server
- I-Mutant 2.0.7 – A Tool for Predicting Protein Stability upon Mutation
- SLiMSuite 20130412 – Bioinformatics Tools to Analyse Protein Features
- PhosSNP 2.0 – Influence of Protein Phosphorylation by nsSNP
- DOG 2.0.1 – Protein Domain Structure Visualization
- PSICOV 1.10 – Accurate Contact Prediction from Large Protein Alignments
- Folding@home 7.3.6 – Understand Protein Folding, Misfolding & Related Diseases
- SIFT 5.0.3 – Amino Acid Substitution Affects Protein Function
- ESpritz 1.3 – Disorder Predictor for High-throughput Application
- MapQuant 2.1.1 – Large-scale Protein Quantification
- SignalP 4.1b – Predict Signal Peptides
- IDEAL-Q 1.063 – Mass Spectrometry Protein Quantitation
- seqsee 1.6 – Protein Sequence Analyzer
- mkdom/Xdom 2 – Build the ProDom Database
- NRPSpredictor2 20111113 – Predict NRPS Adenylation Domain Specificity
- NetSurfP 1.0b – Protein Surface Accessibility & Secondary Structure Predictions
- NetMHCpan 2.4a – Predicts Binding of Peptides to Known MHC Molecule
- NetNGlyc 1.0c – N-linked glycosylation sites in human proteins
- ANTHEPROT 6.3.1 – Protein Sequence Analysis
- PepDistiller 1.26 – Improve Sensitivity & Accuracy of Peptide Identifications in Shotgun Proteomics
- ProPAS 1.1 – Protein Property Analysis Software
- cRacker 1.496 – Analysis tool for Proteomic Datasets (LC-MS/MS)
- protpy 1.0 – Development of Protein Descriptors using Python
- HydroPaCe – Understanding and Predicting Cross-inhibition in Serine Proteases through Hydrophobic Patch Centroids
- CSM – Funciton Prediction and Fold Recognition by Protein inter-residue Distance Patterns
- aCSM – atomic Cutoff Scanning Matrix
- Domain Fishing 1.0 – Look for Recognizable Protein Domains
- PIP – webserver for Potential Protein-protein Interactions
- PAAT 1.1 – Peptide Abundance Analysis Toolbox
- Validate Fasta File 2.1.4808 – Parse Fasta file and return the number of proteins and number of Residues
- STEPP 1.0 – SVM Technique for Evaluating Proteotypic Peptides
- SCX Prediction Utility 2.2.3994 – Strong Cation Exchange Elution Time Prediction Utility
- Protein Sequence Motif Extractor 1.0.4752 – Look for the specified Motif in each Protein Sequence
- NETPredictionUtility 2.2.4178 – Normalized Elution Time Prediction Utility
- Protein Digestion Simulator 2.2.4798 – Read a Text file containing Protein sequences and output the data to a Tab-delimited file
- FastaFileComparer 1.2.4786 – Compares Protein Sequences from two different Fasta files
- Protein Coverage Summarizer 1.3.4798 – Determine Percent of Residues in Protein Sequence
- Protemot – Prediction of Protein Binding sites with automatically extracted Geometrical Templates
- MEDock – Web Server for Efficient Prediction of Ligand Binding sites
- PRASA – Analyze Protein Interaction types
- DBD2BS – Connecting a DNA-binding Protein with its Binding Sites
- acACS 1.0 – Auto Covariance of Average Chemical Shifts
- KNN-ID – Classifier for Discriminating Thermophilic and Mesophilic Proteins
- PreDNA 1.0 – Accurate Prediction of DNA-binding sites in Proteins
- OrFin – Webserver For Finding Orthologs For Two Organisms
- AmylPepPred – Amyloidogenic Peptide Prediction tool
- ExonVisualiser – Exon Identification & Visualization in Protein Structures
- AnaGram – Protein Function Prediction
- SSP – Secondary Structure Propensity
- ENSEMBLE – Generate Structural Models of the unfolded state
- Predikin – Predict Substrate Specificity of Protein Kinases
- PREDIVAC – CD4+ T-cell Epitope Prediction for Vaccine Design
- iMembrane – Homology-Based Insertion of Proteins into the Membrane
- MEDELLER – Homology-Based Coordinate Generation for Membrane Proteins
- FREAD 3.0.1 – Database Search Loop Structure Prediction protocol
- SPEPLip – Predictor of Signal Peptide and Lipoprotein Cleavage Sites in Proteins
- CCHMMPROF – Predictor of Coiled-Coils Regions in Proteins Exploiting Evolutionary Information
- PS-COILS 1.0 – Coiled-coil Predictor
- PCOILS 1.0.1 – New COILS version that uses Profiles as inputs
- BetAware – Beta-Barrel Detection and Topology Prediction
- phoMSVal 1.0.1 – Managing MS/MS data and automatically Validating Identified Phosphopeptides
- PIE 0.35 / PIE-Web – Protein Inference Engine
- MEME 4.9.0 – Discovering Motifs within the Sequences
- mMass 5.4.1 – Open Source Mass Spectrometry Tool
- CCCP – Coiled-coil Crick Parameterization
- MaDCaT – Protein Structure Search tool
- DrawCoil 1.0 – Produce Coiled-coil Helical Wheel Diagrams
- CLEVER 1.0 – Sequence based Approximation of Protein Energies
- HARBP 1.0 – Predicting Binding Activity of influenza virus Hemagglutinin(HA) to human and avian Receptors
- NCACO-score 1.0 – Main-chain dependent Scoring Function for Structure Modeling
- RASP 1.78 – RApid Side-chain Predictor
- CISRR 1.01 – Prediction of Side-chain Modeling
- T3SEpre – T3S effector Prediction model based on joint features including Aac, Sse and Acc
- BPBAac – T3S effector prediction tool based on position-specific Amino Acid composition features in N-termini
- PCP 1.0 – Protein Complex Prediction
- MetaPepSeq 0.8 Beta – Protein Identification in Mass Spectrometry Experiments.
- FSWeight 2.2 – Protein Function Prediction
- ADDA version 4 – Automatic Domain Decomposition Algorithm
- GTG – Remote Homology Detection and Fold Assignment
- PDEXK – Server for Detection of new Protein Families from the PD-(D/E)XK Superfamily
- SoDA / SoDA2 – Somatic Diversification Analysis
- ProDGe 20110509 – Investigate Protein-protein Interactions at the Domain level
- SABINE 1.2 – Prediction of the Binding Specificity of Transcription Factors using Support Vector Regression
- TFpredict 1.1 – Identification and Structural Characterization of Transcription Factors
- parse-mif25 1.0 – Parse Protein-protein Interaction data in MIF v2.5 format
- Papia – Protein Information Analysis System
- GRIFFIN – G-protein and Receptor Interaction Feature Finding INstrument
- JOY 5.0 – Protein Sequence-Structure Representation and Analysis
- 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
- ASAView – Solvent Accessibility Graphics for Proteins
- Qgrid – Identify Clusters of Charged and Hydrophobic Regions in Proteins
- CCRXP – Identifies Clusters of Conserved Residues in Proteins using PDB files
- DBS-PRED – Prediction of DNA-binding in proteins using Neural Networks
- DBS-PSSM v3 – Predicts DNA-binding sites in Proteins
- ReadOut – Calculation of Direct and Indirect Readout energy Z-scores for Protein-DNA complexes
- SDCPRED – Specific DNA COntact Prediction
- POLYVIEW-2D / POLYVIEW-3D / POLYVIEW-MM – Protein Structure Annotation using Sequence Profiles / Structures / Motions
- PhoScan – Prediction of Kinase-specific Phosphorylation sites
- SubMito 1.1 – Predict Protein Submitochondria Locations from Sequence
- EPO – Enhanced Partial Order Curve comparison over Multiple Protein Folding Trajectories
- LFM-Pro – Detection of Significant Local Structural Sites in Proteins
- FOLD-RATE – Prediction of Protein Folding Rates from Amino Acid Sequence
- DISC-FUNCTION – Functional Discrimination of Membrane Proteins
- DNAbinder – Prediction of DNA-binding Proteins
- CUPSAT – Protein Stability Analysis Tool
- TMDET 2.0 – Detection of Transmembrane Regions of Membrane Protein
- SCPRED – Prediction of Stabilization Centers in Proteins
- DNAbind – DNA Binding Protein prediction
- DAS-TMfilter – On filtering False Positive Transmembrane Protein Prediction
- SCide – Identification of Stabilization Centers in Proteins
- SRide – Identification of Stabilizing Residues in proteins
- TMBETA-NET – Discrimination and Prediction of Transmembrane Beta Strands in Outer Membrane Proteins
- FORTE – Profile-profile Comparison tool for Protein Fold Recognition
- POODLE – Prediction Of Order and Disorder by machine LEarning
- Pcons – Protein Structure Prediction Meta Server
- refolding 0.1 – Tools for Protein Unfolding and Refolding under the AFM
- AdaPatch 1.0 – Searche for Dense and Spatially Distinct Clusters of sites
- MinRMS – A Tool for Determining Protein Similarity
- K-Pax – Bayesian unsupervised Classification of Protein Sequences
- SurpResi 201108 – Protein Active Site Prediction based on Central Distances of Amino Acids
- SPIDER – Scoring Protein Interaction Decoys using Exposed Residues
- DLocalMotif – Discover Local Motifs in Protein Sequences
- Continuum Secondary Structure Predictor
- Protein Prowler 1.2 – Subcellular Localisation Predictor
- JSUBST – Building Environment-Specific Substitution Tables
- iPATCH – Prediction of Inter-protein Contact sites
- SOCKET 3.03 – Identifies Knobs-into-holes packing in Protein Structures
- SCORER 2.0 – Distinguish Parallel Dimeric and Trimeric Coiled-coil Sequences
- LOGICOIL – Multi-state Coiled-coil Oligomeric State prediction
- transFold – Super-secondary Structure Prediction of Transmembrane β-barrel proteins
- SSPred – Identification & Classification of Proteins involved in Bacterial Secretion Systems
- PyNISTPL – Python module that Interfaces to the NIST MS Search Engine libraries
- GlycoPeptideSearch 1.3.5 – Interpretation of N-glycopeptide by searching for Glycopeptide Results consistent with MS/MS spectra
- ALL-P – Including shared Peptides for Estimating Protein Abundances
- MassChroQ 2.0 – Mass Chromatogram Quantification
- DeNovo Pipeline 1.4.2 – Protein Identification by de novo Interpretation
- X!TandemPipeline 3.3.0 – Peptide / Protein Identifications from MS/MS Mass Spectra
- IPRStats 0.4.2 – Visualization of Interproscan Results
- InterProScan 5 RC4 – Protein Domains Identifier
- SAMP – Structural Annotation of Malaria proteins
- SVM-FOLD – Web Tool for Protein Structural Classification
- ConSurf 2010 – Identification of Functional Regions in Proteins
- Epitopia – Detection of Immunogenic Regions in Protein Sequences
- rate4site 2.01 – Detect Conserved Amino-acid Site
- VitaPred – Prediction of Vitamin Interacting Residues
- SBSPKS – Structure Based Sequence Analysis of Polyketide Synthases
- 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
- VGIchan – Voltage Gated Ion Channel Prediction server
- SRTpred – SVM based method for Prediction of Secrteory Proteins
- MitPred 2.0 – Predict Mitochondril Proteins
- BTXpred – Prediction of Bacterial Toxins
- MANGO – Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)
- PSLpred – SVM based method for the Subcellular Localization of Prokaryotic Proteins
- HSLpred – SVM based method for Teh Subcellular Localization of Human Proteins
- GPCRSclass – SVM based Classification of Amine Type of GPCR
- GPCRpred – Prediction of Families & Superfamilies of G-protein Coupled receptors
- NRpred – SVM based method for Prediction of Nuclear Receptors
- ESLpred – Subcellular Localization of Eukaryotic Proteins
- ABAG – Computation of Antibody/Antigen Concentration and Endpoint Titer
- CTLPred – SVM & ANN Based CTL epitope Prediction method
- TAPPred – Predict Peptide TAP Binding Affinity
- MHC – Matrix Optimization Technique for Predicting MHC binding Core
- Pcleavage – SVM based 20S Proteasomal Prediction Method
- MHC2Pred – SVM based method for MHC class II Binders Prediction
- MMBPred – Predict Mutated MHC Binders
- ABCpred – Artificial Neural Network based B-cell Epitope Prediction Server
- HLADR4Pred – SVM and ANN based HLA-DR Bininding Peptide Prediction
- nHLAPred – Neural Network based MHC Class-I Binding Peptide Prediction Server
- BcePred – Predict B cell Epitope based on Physio-chemical Properties of Amino Acids
Recent Comments