protein analysis fwd

Again, a lot of information, but better there are some things you can choose than nothing to choose.

Protein analysis:

• 3MATRIX 1.0 – Motif in 3D
• 3MOTIF 2.0 – Motif in 3D
• Alphabet – Find Groups of Amino Acids that Co-occur in Columns Frequently
• Anchor – Predict Binding Regions in Proteins
• annot8r_physprop 0.1 – Predict Physical Properties of Peptides
• ANTHEPROT 6.0 – Protein Sequence Analysis
• APAT 1.4.1 – Automated Protein Annotation Tool
• APEX 1.1.0 – Quantitative Proteomics Tool
• assp 1.2 – Assess Protein Secondary Structure Prediction Accuracy
• BepiPred 1.0b – Linear B-cell epitopes
• BSpred – Predict Binding Site of Proteins
• CDPred 1.01 – Conserved Domain-based Prediction
• ChloroP 1.1 – Predict Chloroplast Transit Peptides
• CLANS 20101007 – Visualize Protein Families based on Pairwise Similarity
• CLC Protein Workbench 5.5.2 – Workbench for Protein Analysis
• CoBaltDB 1.0 – Complete Bacterial and Archaeal Orfeomes Subcellular Localization Database
• ConTest 1.0.1 – Test Constraints in Proteins
• CRC64 2006 – Improved 64-bit Cyclic Redundancy Check for Protein Sequences
• CS-PSeq-Gen 1.0 – Simulation of Protein Sequences under Constraints
• DASher 1.3.4 – Protein Sequence Client for DAS
• dasty 3.0.0.8 – Visualize Protein Sequence Feature Information using DAS
• DEPTH 2.8.7 – Measure Extent of Atom/Residue Burial within Protein
• DICROPROT 2000 – DICHROism of PROTeins
• DISCO 1.0 – Structure Determination of Protein Homo-oligomers
• DiscoTope 1.1a – Predicts Discontinuous B cell Epitope
• Discriminative HMMs – Find Discriminative Motif to Predict Protein Subcellular Localization
• DisEMBL 1.5 – Protein Disorder Prediction
• DISOPRED 2.43 – Intrinsic Protein Disorder Prediction
• DomainFinder 2.0.4 – Determine Dynamical Domains in Protein
• eBLOCKS – Database of Conserved Protein Regions
• EFICAz2 1.3 – Accurate Sequence based Approach to Enzyme Function Inference
• eSIGNAL 1.0 – Database of Medline MeSh Terms & Protein Motifs that Detect Signal Transduction Proteins
• estzmate – Assess Potential for Protein Coding Region
• FFAS 03 – Pretein Structure Prediction based on Profile-profile Comparison
• Folding@home 6.23 – Understand Protein Folding, Misfolding & Related Diseases
• FoldMiner 200312 – Structural Similarity Searches and Motif Discovery
• GPMAW 9.10 – Mass Spectrometric Analysis of Proteins and Peptides
• greylag 0.2.2 – Tandem Mass Spectrum Peptide Identification and Validation
• HBAT 1.1 – Hydrogen Bond Analysis Tool
• HMMER 3.0 – Protein Sequence Homology Search
• HMMSTR 20091212 – Protein Secondary Structure Prediction
• HMMSTR-CM – Protein Contact Map Prediction
• HMMSUM – Structure-based Substitution Matrices
• HMMTOP 2.9 – Predict Transmembrane Helices and Topology of Proteins
• Hydrophobicity – Display Hydropathic Character of Protein
• I-sites 2 – Predict the Local Structure of a Protein
• I-TASSER 1.1 – Protein Structure & Function Predictions
• InteroPorc 2.0.2 – Automatic Molecular Interaction Predictions
• InterProScan 5 – Protein Domains Identifier
• InterViewer 4.0 – Visualize Large-scale Protein Interaction Networks
• IUPred – Predict Intrinsically Unstructured Regions of proteins
• Jali 1.3 – Remote Homology Detection for Protein
• Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0 – Multiple Sequence Alignment , Viewer & Quality Assessment
• LipoP 1.0a – Prediction of Lipoproteins & Signal Peptides in Gram Negative Bacteria
• MASKER – Molecular Surface Area Calculator
• MDT 5.1 – Prepares a raw Frequency Table
• MEME 4.7.0 – Discovering Motifs within the Sequences
• MEMPACK – SVM Prediction of Membrane Helix Packing
• MEMSAT 3 – Transmembrane Protein Structure Prediction
• MEMSAT-SVM – SVM Transmembrane Protein Structure Prediction
• MetaTM 1.1 – Predicte Transmembrane Topology
• mkdom/Xdom 2 – Build the ProDom Database
• MODELESTIMATOR 1.1 – Estimate Amino Acid Replacement Rates
• MPEx 3.2 – Tool for Exploring Membrane Proteins
• MPtopoQuerier – Search Database of Membrane Proteins
• MultiLoc2 20091026 – Predict Animal, Plant and Fungal Protein Subcellular Localization
• NAP – Nucleotide Amino Acid Alignment
• NASCA 20110516 – Side-chain Resonance Assignment & NOE Assignment
• NetCGlyc 1.0c – Predict C-mannosylation
• NetChop 3.1b – Neural Network Predictions for Cleavage Sites of Human Proteasome
• NetCTL 1.2a – Predict CTL Epitopes in Protein Sequence
• NetMHC 3.0c – predict Binding of Peptides to MHC Class I Alleles
• NetMHCII 2.2 – Predict Binding of Peptides to MHC class II Alleles
• NetMHCIIpan 2.0a – predict Pan-specific Binding of Peptides to MHC class II HLA-DR Alleles
• NetMHCpan 2.4 – Predicts Binding of Peptides to Known MHC Molecule
• NetNGlyc 1.0a – N-linked glycosylation sites in human proteins
• NetOGlyc 3.1d – Predict Mucin-type O-glycosylation
• NetPhos 3.1 – Generic Phosphorylation Sites in Eukaryotic Proteins
• NetSurfP 1.0 – Protein Surface Accessibility & Secondary Structure Predictions
• NOXclass – Prediction of Protein-protein Interaction Types
• NQ-Flipper 2.7 – Validate Asparagine and Glutamine Side-chain Amide Rotamers in Protein Structures
• NRPSpredictor2 20110911 – Predict NRPS Adenylation Domain Specificity
• NucImport – Nuclear Protein Import and Localisation Signals Predictor
• NucPred 1.1 – Predicting Nuclear Localization of Proteins
• OSPREY 1.0 – Computational Structure-based Protein Design
• Osprey 1.2.0 – Protein-protein Interaction Networks Visualization System
• PairwiseStatSig 20081215 – Pairwise Statistical Significance
• PexSPAM 1.2 – Protein Sequence Feature Extraction
• pfilt – Sequence Filtering for Low-complexity, Coiled-coil and Biased Amino Acid Regions
• pGenTHREADER 8.7 – Protein Fold Recognition by Profile-profile Threading
• Phobius /PolyPhobius 1.05 – Combined Transmembrane Topology & Signal Peptide Predictor
• PISCES 1.0 – Protein Sequence Culling Server
• PIVOT 2.0 – Protein Interactions VisualizatiOn Tool
• PoSSuM / PoSSuMsearch 2.0 – Matching of PPSSMs using Enhanced Suffix Arrays
• Pratt 2.1 – Find Flexible Patterns in Unaligned Protein Sequences
• ProBias/BIAS – Detect Compositional Bias in Biological Sequences
• ProCon 1.1 – Localization & Visualization of Protein Conservation
• ProCope 1.2 – Protein Complex Prediction and Evaluation
• ProP 1.0c – Arginine & Lysine propeptide Cleavage Sites in Eukaryotic Protein
• ProQ 1.2 – Protein Quality Predictor
• ProTag 1.4 – Office Add-In for offering SmartTag of Protein
• PROTEAN – Torsion Space Molecular Simulations
• Protein Coverage Summarizer 1.3.4053 – Determine Percent of Residues in Protein Sequence
• ProteinVis 2.1.6 – Tree viewer for Hierarchical Clusterings of Proteins
• ProteoWizard 2.0 – Proteomics Data Analysis
• PROTMAP2D 1.2.2 – Calculation, Visualization & Comparison of Contact Map
• PSAAM – Protein Sequence Analysis And Modelling
• PSI Protein Classifier 1.0.1.49 – Automation of the PSI-BLAST Results Analysis
• PSIPRED 3.21 – Accurate Protein Secondary Structure Prediction
• PSORTb 3.0.3 – High-precision Localization Prediction for Bacterial Proteins
• PSSpred 1.0 – Multiple Neural Network Training program for Protein Secondary Strucure Prediction
• ps_scan 1.75 – PROSITE scanning program
• PyRosetta 2.0 – Python-based Interface to Rosetta Molecular Modeling Suite
• RDC-PANDA 1.0 – NMR NOE Assignment & Protein Structure Determination
• REPRO – Protein Repeats Analysis
• Rosetta 3.3 – Simulation and Design of Protein
• RW 1.0 – Protein Structure Modeling and Structure Decoy Recognition
• SAPTF 1.7 – Sequence Analysis Plugin Tool Framework
• SCANPS 2.3.11 – Protein Sequence Scanning Package
• SCWRL 4.0 – Prediction of Protein Side-chain Conformation
• SecretomeP 2.0 – Prediction of Non-classical Protein Secretion
• Sfixem – SFS Visualisation Tool in Java
• SherLoc2 20091026 – Predicting Protein Subcellular Localization
• SIFT 4.0.4 – Amino Acid Substitution Affects Protein Function
• SignalP 4.0c – Predict Signal Peptides
• SMAP 2.0 – Comparison & Similarity Search of Protein Three-dimensional Motif
• SPICE 0.9 – Protein Sequences, Structures & Annotations Browser
• SPICKER 20101229 – Cluster Protein Structures for Near-native Model Selection
• STORM 1.01 – Protein Analyses of BLAST, FASTA, Pfam and ProtParam
• SubMito 1.1 – Predict Protein Submitochondria Locations from Sequence
• SVMSEQ 1.0 – Protein Contact Prediction
• TargetP 1.1 – Predict Protein Subcellular Localisation
• TESTLoc – Protein Localization Prediction based on ESTs
• TM-score 20110130 – Calculate Similarity of Topologies of two Protein Structures
• TMHMM 2.0c – Prediction of Transmembrane Helices in Proteins
• Topcons – Consensus Prediction of Membrane Protein Topology
• TOPO2 – Create Transmembrane Proteins Images
• TRUST 1.0 – Repeat Detection Method
• Utopia 1.4.5 – Protein Analysis Suite
• VDJsolver 1.0b – Analysis of Human Immunoglobulin VDJ Recombination
• VEMS 5.18042011 – Analysis of MS-based Proteomics Data
• VHMPT – Viewer & Editor for Helical Membrane Protein Topologies
• WinPep 3.01 – Analysis of Aminoacid Sequences
• Wise 2.2.0 – Compare Protein Sequence to Genomic DNA Sequence
• YinOYang 1.2 – O-(beta)-GlcNAc Glycosylation and Yin-Yang Sites