Posts
- Category: Protein Sequence Analysis (continued)
- DNAbinder - Prediction of DNA-binding Proteins
- DNABindProt - Server for Determination of Potential DNA Binding Sites of Proteins
- DoBi 1.5 - Predicting the Binding Sites on pair of given Proteins
- DockRank - Rank Docked Models Using Predicted Partner-Specific Protein-Protein Binding Sites
- Domain Fishing 1.0 - Look for Recognizable Protein Domains
- DomainFinder 2.0.4 - Determine Dynamical Domains in Protein
- DomainParser 2 - Protein Structure Domain Partition
- DomEx - Extending Protein Domain Boundary Predictors
- DOMIRE - DOMain Identification from Recurrence
- DoMo-Pred - Domain-Motif Mediated Interaction Prediction
- DoMosaics 0.95 - Domain-centric Analysis of Proteins
- DOMpro 1.0 - Protein Domain Prediction
- DomStratStats v1.05 - Compute per-protein Domain Family q-values and local FDRs
- doublet 1.0 - Incorporate Patterns of Dipeptide Covariation to Align Protein Sequences
- Dover Analyzer 0.1.2 - Overlap and Diversity in Antimicrobial Peptide Database
- dPABBs - Predicting and Designing Anti-biofilm Peptides
- DPD - Identification and Quantification of the Protein
- DPPI - Convolutional Neural network to predict PPI Interactions
- DPROT - Prediction of Disordered Proteins
- DPUC 2.08 - Using Context to Improve Protein Domain Identification
- DrawCoil 1.0 – Produce Coiled-coil Helical Wheel Diagrams
- dRHP-PseRA - Detecting Remote Homology Proteins using Profile-based Pseudo Protein Sequence and Rank Aggregation
- DSPMP - Discriminating Secretory Proteins of Malaria Parasite
- DSSP 2.2.1 - Calculates DSSP Entries from PDB Entries
- DUET - Predicting Effects of Mutations on Protein Stability
- DynaFace - Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions
- DynaMine Beta - Predicting Protein Dynamics from Sequence
- e-Driver - Identify Protein Regions driving Cancer
- EagleEye 1.66 - Remove Background MS/MS Spectra
- eBLOCKS - Database of Conserved Protein Regions
- eCAMI - Simultaneous Classification and Motif Identification for enzyme/CAZyme annotation
- EDCNN -Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network
- EFC-FCBF - Framework for Feature Construction and Selection for Improved Recognition of Antimicrobial Peptides
- EFI-EST - Generating Protein Sequence Similarity Networks
- EFICAz 2.5 - Accurate Sequence based Approach to Enzyme Function Inference
- EFIN - Evaluation of Functional Impact of Nonsynonymous SNPs
- ELASPIC - Ensemble Learning Approach for Stability Prediction of Interface and Core Mutations
- ELM / iELM 1.0 - Investigation of Functional Sites in Protein Sequences with Eukaryotic Linear Motif database
- Emap2sec - Protein secondary structure detection in intermediate-resolution cryo-EM maps
- ENCoM - Exploring Protein Conformational Space and Effect of Mutations on Protein Function and Stability
- enDNA-Prot - Identification of DNA-binding Proteins by Applying Ensemble Learning
- EnPPIpred - Enteropathogen Protein Protein Interactions (PPIs) Prediction
- ENSEMBLE - Generate Structural Models of the unfolded state
- ENTPRISE / ENTPRISE-X - Predicting Human Disease-associated Amino Acid Mutations
- EnTrans-Chlo - Transductive Learning for Protein Subchloroplast Localization
- ENZYMAP - Exploiting Protein Metadata for Modeling and Predicting Annotation Changes in UniProt/Swiss-Pro
- EPAD - Context-specific Distance-dependent Statistical Potential for Protein Study
- EPCES - Prediction of Antigenic Epitopes on Protein Surfaces by Consensus Scoring
- EpIC - Epitope Immunogenicity Characterization
- EpiC beta - Identify Target Epitopes for Antibody Design
- EpiDOCK - Molecular Docking - based tool for MHC class II Binding predicition
- EpiJen 1.0 - Multi-step algorithm for MHC class I binding prediction
- EpiPred - B-cell Epitope Prediction
- EPISOFT - Epitope Vaccine Optimization Server
- EpiTOP 3.0 - Proteochemometrics-based tool for MHC class II Binding Prediction
- EPITOPEFINDER 0.11 - Finding Immune Epitopes
- Epitopia - Detection of Immunogenic Regions in Protein Sequences
- eProS - Analysis of Protein Energy Profiles
- EPSVR / EPMeta - Prediction of Antigenic Epitopes
- Erebus - Protein Substructure Search Server
- eSIGNAL 1.0 - Database of Medline MeSh Terms & Protein Motifs that Detect Signal Transduction Proteins
- ESLpred2 - Subcellular Localization of Eukaryotic Proteins
- ESpritz 1.3 - Disorder Predictor for High-throughput Application
- estzmate - Assess Potential for Protein Coding Region
- EvoDesign - Evolutionary profile based approach to de novo Protein Design
- ExonVisualiser - Exon Identification & Visualization in Protein Structures
- EzyPred - Predicting Enzyme Functional Classes and Sub-classes
- FaaPred - Fungal Adhesins and Adhesin-like proteins Predictor
- FANN-GO - Predict Gene Ontology terms for a given protein sequence
- FastaFileComparer 1.2.4786 - Compares Protein Sequences from two different Fasta files
- FastHMM / FastBLAST 1.3 - Analyzing Large Protein Sequence Databases
- FastMG 20140909 - Estimate Amino Acid Substitution Matrices for large data sets
- fastSCOP - Protein Structure Evolutionary Classifications
- FATHMM 2.3 / FATHMM-MKL - Predicting the Functional Effects of Protein Missense Mutations
- FCP - Functional Coverage of the Proteome by Structures
- FDDH - pKa calculations with the FD/DH method
- Fetchdom 3.0 - Dig the Data into the ProDom files
- FFAS 03 - Pretein Structure Prediction based on Profile-profile Comparison
- FingerPRINTScan - PRINTS Fingerprint Search Tool
- FIRE-pro 1.1 - Motif Discovery and Characterization program in Proteins based on Mutual Information
- firestar - Predicting Functional Residues from Structural Templates and Alignment Reliability
- Fitmunk - Improving Protein Structures by accurate, automatic Modeling of Side-chain Conformations
- FlexServ - Analysis of Protein Flexibility
- FoldAmyloid - Prediction of Amyloidogenic Regions from Protein Sequence
- Folding@home 7.6.21 - Understand Protein Folding, Misfolding & Related Diseases
- FoldMiner 200312 - Structural Similarity Searches and Motif Discovery
- FoldRec-C2C V1 - Protein Fold Recognition by combining Cluster-to-cluster model and Protein Similarity Network
- FoldUnfold - Prediction of Disordered Regions in Protein Chain
- FORA - Prediction of Protein Folding Rate Change
- Forcefield_NCAA - AMBER Forcefield Parameters for Non-canonical Amino Acids
- Forcefield_PTM - AMBER Forcefield Parameters for Post-translational Modifications
- Frag'r'Us - Extract and Characterize Supersecondary, or Smotifs from Protein Structures
- FRAGSION 1.0 - Protein Fragment Library Generation
- Framedp 1.22 - Sensitive Peptide Detection on Noisy Matured Sequences
- FREAD 3.0.1 - Database Search Loop Structure Prediction protocol
- FreeContact 1.0.21- Protein Contact Prediction from Residue Co-evolution
- Freescore - Classification of Conotoxin Proteins
- FRST 1.2 - Protein Model Quality Estimation Method
- FSWeight 2.2 - Protein Function Prediction
- FT-ARM - Identification and Quantification of Multiplexed High-resolution
- FUEL-mLoc - Feature-Unified Prediction and Explanation of multi-Localization of Cellular Proteins in multiple Organisms
- FUGUE 20160606 – Protein Structure Prediction using Remote Homology Detection
- FUSION - de novo Protein Structure Prediction
- G-effector - A Predictor on the Effector of Heterotrimeric G proteins
- GammaPred - Prediction of Gamma-turns in Proteins using Multiple Alignment and Secondary Structure Information
- GAP - Distinguishing between Amyloid Fibril-forming and Amorphous β-aggregating Aggregation-prone Regions
- GAPlus - An Enhanced Genetic Algorithm (GA) for lattice based Protein Structure Prediction
- GASS - Identifying Enzymes Active Site with Genetic Algorithms
- GlobPlot / GlobPipe 2.3 - Explore Disorder or Globularity in Protein Sequences
- GLYCO - Quantify Glycan Shielding of Glycosylated Proteins
- GlycoEP - Prediction of Glycosysylation sites in Eukaryotics Proteins
- GlycoMine - Predicting N-, C- and O-linked glycosylation in the Human Proteome
- GlycoPeptideSearch 1.3.12 - Interpretation of N-glycopeptide by searching for Glycopeptide Results consistent with MS/MS spectra
- GlycoPP 1.0 - Prediction of Glycosites in Prokaryotic Protein Sequences
- GoCore 5.0.1 - Protein Sequence Alignment and Analysis
- GOMoDo beta - GPCR Online MOdeling and DOcking server
- GPCR-2L - Predicting G-protein coupled Receptor attribute at two levels
- GPCR-CA - Predicting GPCR Classification
- GPCR-GIA - Predicting GPCR Classification
- GPCRHMM - GPCR detection method
- GPCRpred - Prediction of Families & Superfamilies of G-protein Coupled receptors
- GPCRSclass - SVM based Classification of Amine Type of GPCR
- GPMAW 12.5 - Mass Spectrometric Analysis of Proteins and Peptides
- GprotPRED - Detection of distinct Galpha families, Gbeta and Ggamma subunits of heterotrimeric G-proteins
- GPS 5.0 - Kinase-specific Phosphorylation Site Prediction
- GPS-ARM 1.0 - Prediction of D-boxes and KEN-boxes
- GPS-CCD 1.0 - Computational Predictioin of Calpain Cleavage Sites
- GPS-MBA 1.0 - MHC-binding Analyzer
- GPS-Polo 1.0 - Prediction for Polo-like kinases
- GPS-PUP 1.0 - Prediction of Pupylation Sites
- GPS-SNO 1.0 - S-nitrosylation Sites Prediction
- GPS-YNO2 1.0.1 - Prediction of Tyrosine Nitration Sites
- Gram-LocEN - Interpretable prediction of subcellular multi-localization of Gram-positive and Gram-negative bacterial proteins
- Graphlet kernel 1.01 - Annotate Functional Residues in Protein Structures
- GraphPAC 1.34.0 - Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach
- GraphProt 1.1.4 - Modeling Binding preferences of RNA-binding Proteins
- greylag 0.2.2 - Tandem Mass Spectrum Peptide Identification and Validation
- GSTPred - Prediction of Glutathione S-transferase Proteins
- GTPbinder - predicting GTP interacting Residues in a Protein
- H-Protection - Prediction of Residue Status to be protected or unprotected from Hydrogen-deuterium Exchange
- H2r - Identification of Evolutionary Important Residues
- HBAT 1.1 - Hydrogen Bond Analysis Tool
- HBPred 2.0 - Identification of Hormone-binding Protein
- HDXanalyzer 1.0 - Statistical Analysis of Protein Structure Dynamics
- HEA-PSP - Ab-initio Protein Structure Prediction
- Helical wheel tool - Represent a Protein Sequence as a Helical Wheel diagram
- Helix Packing Pair - Calculation of Helix Packing Angles in Protein Structures
- HelixCorr 20081105 - Predict interacting Transmembrane Helices
- HemeBIND / HemeBIND+ - Heme Binding Residue Prediction from Protein Sequence and Structure
- HemeNet - Heme Binding Residue Prediction using Sequence, Structure, and Residue Interaction Network
- HemoPI - Computing Hemolytic Potency of Peptides
- hfAIM - High Fidelity Autophagy-associated atg8-interacting Motifs detecting tool
- HH-suite v3.3.0 - Remote Protein Homology Detection suite
- HIPPIE - Protease Inhibitor engine
- Hipsec 2.0 - Predict High-level Protein Production in Aspergillus Niger
- HITS-PR-HHblits - Protein Remote Homology Detection by Combining PageRank and Hyperlink-Induced Topic Search
- HIVcleave - Predicting HIV Protease Cleavage Sites in Proteins
- HIVcoPRED - Prediction of HIV Coreceptor Usage
- HLADR4Pred - SVM and ANN based HLA-DR Bininding Peptide Prediction
- HLP - Predicting Half-life of Peptides in Intestine like Environment
- HMM-TM - Prediction of Transmembrane Alpha-Helical Proteins
- HMMCAS - Identifying Cas Genes and Proteins
- HMMEditor 1.2 - Visual Editor for Profile Hidden Markov Model
- HMMER 3.2.1 - Protein Sequence Homology Search
- HMMpTM - Transmembrane Protein Topology Prediction using Phosphorylation and Glycosylation Site Prediction
- HMMSTR 20120205 - 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
- HOMA - Create Homology models of a protein with unknown Structure
- HotPoint - Hot Spot Prediction Server for Protein Interfaces
- HotSpot - Hot Spot Residues Prediction
- HotSPRing - Hot Spot at Protein-RNA interacing surface
- HPMV - Human (Protein) Mutation Viewer
- HSEpred - Prediction of Half-Sphere Exposure from Protein Sequences
- HSLpred - SVM based method for Teh Subcellular Localization of Human Proteins
- HTJoinSolver 0.4A - Human Immunoglobulin VDJ Partitioning
- HUF-ZINC - HMM-based U-shape Motif Finder for Zinc Binding
- HybridGO-Loc - Multi-Label Protein Subcellular Localization Prediction
- HYCUD 3.3.1 - Prediction of Effective Rotational Correlation Time in Flexible Proteins
- Hydrophobicity - Display Hydropathic Character of Protein
- HyPe - A Peptidoglycan Hydrolase Prediction Tool
- I-Mutant 2.0.7 - A Tool for Predicting Protein Stability upon Mutation
- I-PV 1.43 - CIRCOS module for interactive Protein Sequence Visualization
- I-sites 2 - Predict the Local Structure of a Protein
- I-TASSER 5.1 - Protein Structure & Function Predictions
- iACP - A sequence-based tool for Identifying Anticancer Peptides
- iAFP-Ense - Predict the Antifreeze Protein
- iAMP-2L - Identifying AMPs and their Functional Types
- iATP - Identifying Anti-tubercular Peptides
- iBRET – High Confidence Detection of Protein-protein Interactions in Living Cells
- IBS 1.0.3 - Illustrator of Biological Sequences
- icaars - Identification & Classification of Aminoacyl tRNA Synthetases
- iCataly-PseAAC - Identification of Enzymes Catalytic sites using Sequence Evolution information
- iCDI-PseFpt - Identify the Channel-drug Interaction in Cellular Networking with PseAAC and Molecular Fingerprints
- IceLogo 1.3.8 - Next-generation Visualization of Protein Consensus Sequences
- iCTX-Type - Predicting the types of Conotoxins in Targeting Ion Channels
- iDBPs - Identification of DNA Binding Proteins (DBPs) for Proteins with known 3D-structure
- IDCalc 0.3 - Isotope Distribution Calculator
- IDD Navigator - Similar IDD search
- iDNA-Prot - Predicting DNA-binding proteins
- iDNA-Prot|dis - Identifying DNA-binding Proteins
- iDNAPro-PseAAC - DNA Binding Protein Identification
- IDP-Seq2Seq - Identification of Intrinsically Disordered Proteins and Regions based on Sequence to Sequence Learning
- iDPF-PseRAAAC - Identifying Defensin Peptide Families
- IDRBind - Protein Interface Predictor for Binding Sites of intrinsically disordered protein regions
- iDRBP_MMC - Identifying DNA-binding proteins and RNA-binding proteins
- IDRBP-PPCT - Identifying Nucleic Acid-binding Proteins
- iDrug-Target - Web-services for Predicting Drug-target Interaction
- IFNepitope - Predicting and Designing Interferon-gamma inducing Epitopes
- iGPCR-Drug - Predicting Drug-GPCR Interaction in Cellular Networking
- IGPred - Identifying Immunoglobulins
- iGPS 1.0.1 - Prediction of Site-specific Kinase-substrate Relations from Phosphoproteomic data
- IgSimulator - Versatile tool for Simulation of Immunoglobulin Repertoire
- iHSP-PseRAAAC - Identifying the Heat Shock Protein Families
- iHyd-PseAAC - Predicting Hydroxyproline and Hydroxylysine in Proteins
- iHyd-PseCp - Predict the Identifying Protien Hydroxylation Sites
- ILbind - Consensus-based Inverse Ligand Binding Predictor
- iLIR 1.0 - In silico Identification of Functional LC3 Interacting Region Motifs
- iLoc-Cell - Predictors for Subcellular Localtions of Proteins
- iLoops - Protein-protein Interaction prediction server based on Structural Features
- IMAAAGINE - Search Hypothetical 3D Protein Arrangement in Protein Data Bank
- iMem-Seq - Predicting Membrane Proteins Types
- iMembrane - Homology-Based Insertion of Proteins into the Membrane
- iMethyl-PseAAC - Predict Methylation sites in Proteins
- ImmunoSPdb - Archive of Immunosuppressive Peptides
- INGA 2.0-1 - Protein Function Prediction
- iNitro-Tyr - Prediction of Nitrotyrosine Sites in Proteins with general Pseudo Amino Acid Composition
- Inmembrane 0.95.0 - Prediction of Surface-exposed Proteins in Bacterial Cells
- INPS / INPS-MD - Predictor of the Impact of Non-Synonymous Mutations on Protein Stability from Sequence
- iNR-Drug - Predicting drug-NR interaction in Cellular Networking
- iNR-PhysChem - Identifying Nuclear Receptors and their Subfamilies
- InterMap3D - Predicting and Visualizing Co-evolving Protein Residues
- InteroPorc 2.0.2 - Automatic Molecular Interaction Predictions
- Interpol 1.3.1 - Numerical Encoding and Interpolation of Amino Acid Sequences
- InterPreTS - Interaction Prediction through Tertiary Structure
- InterProScan 5.39-77.0 - Protein Domains Identifier
- InterViewer 4.0 - Visualize Large-scale Protein Interaction Networks
- INTREPED 2.0 - DNA Repair Protein Prediction server
- INTREPID - Prediction of Functionally Important Residues
- iPAC 1.37.0 - Identification of Protein Amino acid mutation Clustering
- iPATCH - Prediction of Inter-protein Contact sites
- iPBA - Protein Structures Mining and Superimposition
- iPhos-PseEn - Predict the identifying human Phosphorylation Sites
- iPhos-PseEvo - Predict the Identifying human Phosphorylated Proteins
- iPPBS-Opt - Identifying Protein-Protein Binding Sites
- iPPBS-PseAAC - Prediction of Protein-Protein Binding Sites
- IPPI - Inferring Protein-Protein Interactions for YEAST
- iPPI-Esml - Identifying Interactions of Proteins
- IPRStats 0.4.2 - Visualization of Interproscan Results
- iPSORT / caml-iPSORT 20100316 - Subcellular Localization Site Predictor for N-terminal Sorting Signals
- IPSSA 1.1.0 - Integrated Positively Selected Sites Analyses
- iPTM-mLys - Identifying multiple Lysine PTM sites and their different types
- IQuant 2.0.1 - A pipeline for Quantitative Proteomics based upon Isobaric Tags
- iSARST / SARST / CPSARST - Rapid Protein Structural Similarity Searches
- ISDTool 2.0 - Predicting ISD of Retroviruses
- iSMP-Grey - Predicting Secretory Proteins of Malaria Parasite Using grey- PsePSSM and SVM
- iSNO-AAPair - Predicting the Cysteine S-nitrosylation Sites in proteins
- iSNO-PseAAC - Predict Cysteine S-nitrosylation sites in proteins
- iStable - Integrated Predictor for Protein Stability change upon Single Mutation
- iSuc-PseAAC - Predicting Lysine Succinylation in proteins by incorporating Peptide Position-specific Propensity
- iSuc-PseOpt - Identifying lysine Succinylation Sites in proteins
- IsUnstruct 2.02 - Prediction of Disordered Residues based on the Ising model
- iUbiq-Lys - Prediction of Lysine Ubiquitination sites in proteins
- IUPred - Predict Intrinsically Unstructured Regions of proteins
- iVKC-OTC - Identifying the Subfamilies of Voltage-gated Potassium Channel
- Jali 1.3 - Remote Homology Detection for Protein
- jEcho 1.0C - An Evolved Weight Vector to CHaracterize the protein's post-translational Modification mOtifs
- jLSTM / LSTM - "Long Short-Term Memory" for Protein Classification
- JOY 5.0 - Protein Sequence-Structure Representation and Analysis
- JPred - Predicting the Types of J-proteins
- JPred 4 - Protein Secondary Structure Prediction Server
- jsPISA 2.0.4 - Protein Interfaces, Surfaces and Assemblies
- JSUBST - Building Environment-Specific Substitution Tables
- K-Pax - Bayesian unsupervised Classification of Protein Sequences
- Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0 - Multiple Sequence Alignment , Viewer & Quality Assessment
- KAPPA 1.1 - Key Amino acid Pattern-based Protein Analyzer
- KiDoQ - Prediction of Dihydrodipicolinate synthase inhibtors using Docking and QSAR
- Kinannote 1.0 - Protein Kinase Identification and Classification
- Kink Finder 1.01 - Find Kinks in Helices
- KNN-ID - Classifier for Discriminating Thermophilic and Mesophilic Proteins
- KNOT 1.0.0 - Detection of Knots in Protein Folds.
- L1pred - Prediction tool for Catalytic Residues in Enzymes
- LabCaS - Prediction of the Calpain Substrate Cleavage Sites
- LactFP - β-Lactamase Fingerprint Prediction Server
- LatPack 1.9.1 - Folding Studies for Arbitrary Lattice Protein Models
- Layers - An Algorithm that Peels Molecule as Layers
- LBtope - Prediction of Linear B-cell Epitopes
- LCR-eXXXplorer - Search, Visualize and Share data for low Complexity Regions in Protein sequence
- LearnCoil / LearnCoil-VMF - Computational Evidence for Coiled-coil-like Motifs in Histidine Kinase Linker Domains /Viral Membrane-Fusion Proteins
- LFM-Pro - Detection of Significant Local Structural Sites in Proteins
- LGEpred - Correlation Analysis and Prediction of Genes Expression from Amino Acid Sequence of Proteins
- LigandRFs - Predict Protein-ligand Binding Sites
- LigSearch - Identification of possible Ligands from 3D Protein Structure or Sequence
- LIPO - Prediction of Lipo-boxes in Gram-negative bacterial Protein Sequences
- LipocalinPred - SVM-based method for Prediction of Lipocalins
- LipoP 1.0a - Prediction of Lipoproteins & Signal Peptides in Gram Negative Bacteria
- LIST - Local Identity and Shared Taxa
- LnLCorr - Detect Pairwise Coevolutionary among Residues in a set of Proteins
- LnSignal - Predicting Protein N-terminal Signal Peptides
- LocNES - Locating Classical NESs in CRM1 Cargo Proteins
- LOCP - Locating Pilus Operons in Gram-positive Bacteria
- LOCPRED - Local Backbone Structure Prediction of Proteins
- loctree3 - Protein Sub-cellular Localization Prediction for all Domains of Life
- LOGICOIL - Multi-state Coiled-coil Oligomeric State prediction
- LogoBar 0.9.12 - Display Protein Sequence Logos
- LOLA 1.36 - Generate Sequence Logos using Position Weight Matrix based Protein Profiles
- LPIcom - Analysis, Comparison and Prediction of Protein Ligand Binding Sites
- LRensemble - LR Ensemble Server for Protein Localization Prediction
- LutefiskXP 1.0.7 / Lutefisk - De novo Interpretation of Peptide CID Cpectra
- Lypred - Predictor for Identifying Bacterial Cell Wall Lyase
- LYRA 1.0 - Lymphocyte Receptor Automated Modelling
- M4T 3.0 - Comparative Protein Structure Modeling
- MaDCaT – Protein Structure Search tool
- MAGIC V1.0.2 / MAGIC-web - Mass Spectrometry-based Automated Glycopeptide IdentifiCation platform
- MALDIPepQuant 3.1 - Quantify MALDI peptides (SILAC) from Phenyx output
- MANGO - Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)
- MAPanalyzer - Analyzing Microtubule-associated Proteins
- MAPP 20050628 - Multivariate Analysis of Protein Polymorphism
- MAPSCI 1.0 - Multiple Alignment of Protein Structures and Consensus Identification
- Marcoil 1.2 - HMM-based Coiled-coil Prediction program
- MarkUs - Assessment of the Biochemical Function for a given Protein Structure
- MARS 1.2 - Robust Automatic Backbone Assignment of Proteins
- MARSpred - Prediction of Mitochondrial Aminoacyl tRNA Synthetases
- MASKER - Molecular Surface Area Calculator
- MASPECTRAS 2.3 - Integrate MS protein Identification
- MASS - Protein Single-Model Global Quality Assessment by Random Forest and Various Energies
- MassChroQ 2.0.1 - Mass Chromatogram Quantification
- MatrixMatchMaker 20121201 - Predicts interacting proteins using Coevolution
- MaxCluster - Protein Structure Comparison and Clustering
- MBPpred - Prediction of Membrane lipid-Binding Proteins using profile Hidden Markov Models
- mCSM - Predicting Effect of Mutations in Proteins using Graph-based Signatures
- MDLoc - A Dependency-Based Protein Subcellular Location Predictor
- MDT 5.5 - Prepares a raw Frequency Table
- MEDELLER - Homology-Based Coordinate Generation for Membrane Proteins
- MEDock - Web Server for Efficient Prediction of Ligand Binding sites
- MeDor 1.4 - Metaserver for Predicting Protein Disorder
- Mem-ADSVM - Multi-Label Membrane Protein Type Prediction
- Mem-mEN - Interpretable Membrane Protein Type Prediction
- MemBrain 20200114 - Transmembrane Protein Structure Prediction
- MEME 5.0.5 - Discovering Motifs within the Sequences
- MemeFinder - Prepare data for use by MEME
- memembed 1.15 - Membrane Protein Orientation Predictor
- MemLoci - Subcellular Localization Predictor for Membrane Proteins
- MEMPACK 2.0 - SVM Prediction of Membrane Helix Packing
- MemPype - Pipeline for Predicting the Topology and the Localization of Membrane Proteins
- MEMSAT 3 - Transmembrane Protein Structure Prediction
- MEMSAT-SVM 1.3 - SVM Transmembrane Protein Structure Prediction
- MemType-2L - Predicting Membrane Protein Types
- MEPI - Predict Catalytic Residues from Protein Structures
- MERCI - Motif EmeRging and with Classes Identification
- MESSA - MEta Server for Protein Sequence Analysis
- Metadisorder - Prediction of Intrinsically Unstructured Proteins (protein disorder) from Amino Acid Sequence only
- MetalDetector 2.0 - Cysteines and Histidines Binding State Predictor
- MetaPred - Prediction of Cytochrome P450 Isoform responsible for Metabolizing a Drug Molecule
- MetaPSICOV 2.0.3 - Precise Structural Contact Prediction
- MetaQuery 1.0.4 - Annotation and Quantitative analysis of Genes in the human Gut Microbiome
- MetaSSPred - Balanced Secondary Structure Predictor
- mFASD - Discriminating Different Types of Metal-binding Sites
- MFDp 2.00 - Prediction of Disordered Residues
- mGOASVM v2 - Multi-Label Protein Subcellular Localization Prediction
- MHC - Matrix Optimization Technique for Predicting MHC binding Core
- MHC-NP - Prediction of Peptides Naturally Processed by the MHC
- MHC2Pred - SVM based method for MHC class II Binders Prediction
- MHCPred 2.0 - Additive method for MHC class I and class II binding prediction.
- MiCroKit 4.0 - An Integrated Database of Midbody, Centrosome and Kinetochore
- MIDAs - Molecular Isotopic Distribution Analysis
- MIEC-SVM 1.1 - Molecular Interaction Energy Component & Support Vector Machine
- Mimox 2 - Comformational B-cell Eitope Prediction tool
- MIMP - Predicting the Impact of Mutations on Kinase-substrate Phosphorylation
- MINNOU - Membrane Protein IdeNtificatioN withOUt explicit use of Hydropathy Profiles and Alignments
- MISTIC - Mutual Information Server to Infer Coevolution
- MitoFates - Identifying Putative Mitochondrial Presequences and Cleavage Sites
- MITOPROT II 1.101 - Prediction of Mitochondrial Targeting Sequences
- MitPred 2.0 - Predict Mitochondril Proteins
- mkdom/Xdom 2 - Build the ProDom Database
- MLAMP - Predicting AMPs Multi-labeled And Unbalanced By Smote-MLKNN
- mLASSO-Hum - Human Protein Subcellular Localization
- MLSTA - Machine Learning Integration for Predicting the Effect of Single Amino Acid Substitutions on Protein Stability
- MMBPred - Predict Mutated MHC Binders
- Mobi 1.1 - NMR Mobility Detection
- MobiDB-lite 3.8.4 - Long Disorder Consensus Predictor
- MOBscan - Automated Annotation of MOB Relaxases
- MODELESTIMATOR 1.1 - Estimate Amino Acid Replacement Rates
- ModelEvaluator 1.0 - Quality Assessment of a Single Model
- MoDL - Find Mutliple Motifs in a set of Phosphorylated Peptides
- ModLink+ - Fold Recognition by using Protein-protein Interactions
- MODPEP - Fast Conformer Ensemble Generator of Protein-bound Peptides
- MoDPepInt 4.8.0 - Prediction of Modular Domain-peptide Interactions
- MoRFCHiBi 1.03 - A MORFs Predictor software tool.
- MoRFpred - Prediction of Short Disorder-to-order Transitioning Binding Regions
- Mosaic 1.05 - a visual framework for Sequence Analysis using N-grams and Spectral rearrangement
- Mosaic Vaccine Designer 1.2.11 - Generate Candidate Vaccine Protein Cocktails that optimize the Coverage
- Motif-All 1.0 - Discovering All Phosphorylation Motifs
- motif-x 1.2 - Biological Sequence Motif Discovery
- MP3 1.0 - Prediction of Pathogenic Proteins in Metagenomic and Genomic Datasets
- MPEx 3.2 - Tool for Exploring Membrane Proteins
- mPLR-Loc - Multi-Label Protein Subcellular Localization Prediction
- MPRAP - Membrane Protein Residue Accessibility Predictor
- MPtopoQuerier - Search Database of Membrane Proteins
- MRFy - Haskell software for Protein Remote Homology Prediction
- MS-ALign 0.7.1.7143 - Find Protein-spectrum Matches
- MS-Cluster 20110327 - Clustering Millions of Tandem Mass Spectra
- MsPI 1.2 - Tool for Protein Identification by PMF
- MulPBA - Multiple Protein Structure Alignment
- Multi-iPPseEvo - Predict the Phophorylation Proteins
- Multi-Q2- Multiplexed Protein Quantitation
- Multi-Relief - Recognize Specificity Determining Residues from Multiple Sequence Alignment
- Multi-VORFFIP / VORFFIP - Predicts protein-, peptide-, DNA- and RNA-binding sites in Proteins
- Multicoil2 - Predicting Coiled Coils and their Oligomerization states
- MULTICOM / MULTICOM Toolbox - Protein Tertiary Structure Prediction
- MultiLoc2 20091026 - Predict Animal, Plant and Fungal Protein Subcellular Localization
- MULTIPRED2 - large-scale Screening of allele-, genotype-, and supertype-specific HLA Associated Peptides
- MUPRED - Protein Secondary Structure Prediction
- MUpro 1.1 - Prediction of Protein Stability Changes for Single Site Mutations from Sequences
- MUSI - MUltiple Specificity Identifier
- Musite 1.0.1 - Prediction of Both General and Kinase-specific Protein Phosphorylation Sites
- MutPred2 - Predicting whether an Amino Acid Substitution in a protein is Deleterious or Neutral
- MycoMemSVM - Identification of Mycobacterial Membrane Proteins
- MycoSec - Identifying Secretory Protein of Mycobacterial proteins
- Mycosub - Predicting Subcellular Localization of Mycobacterial Proteins
- NADbinder - Prediction of NAD interacting residues in proteins
- NAGbinder - Web Server for Predicting N-Acetylglucosamine Binding Sites
- NAP - Nucleotide Amino Acid Alignment
- NASCA 20110516 - Side-chain Resonance Assignment & NOE Assignment
- NCBRPred - Predicting Nucleic Acid Binding Residues in Proteins based on multi-label Learning
- nDNA-prot - DNA-binding Proteins Identification
- NESmapper 1.1 - Prediction of CRM1-dependent Nuclear Export Signals
- NETASA - Prediction of Solvent Accessibility using Neural Networks
- NetCGlyc 1.0c - Predict C-mannosylation
- NetChop 3.1d - Neural Network Predictions for Cleavage Sites of Human Proteasome
- NetCSSP 20200622 - Neural networks for calculating Contact-dependent Secondary Structure Propensity
- NetCTL 1.2b - Predict CTL Epitopes in Protein Sequence
- NetMHC 4.0 - predict Binding of Peptides to MHC Class I Alleles
- NetMHCII 2.3 - Predict Binding of Peptides to MHC class II Alleles
- NetMHCIIpan 3.2 - predict Pan-specific Binding of Peptides to MHC class II HLA-DR Alleles
- NetMHCpan 4.0 - Predicts Binding of Peptides to Known MHC Molecule
- NetNGlyc 1.0 - N-linked glycosylation sites in human proteins
- NetOGlyc 4.0 - Predict Mucin-type O-glycosylation
- NetPhos 3.1 - Generic Phosphorylation Sites in Eukaryotic Proteins
- NetSurfP 2.0 - Protein Surface Accessibility & Secondary Structure Predictions
- NeuroPID 201503 - Neuropeptide-Precursor Identifier
- NeuroPIpred - Tool to Predict, Design and Scan Insect Neuropeptides
- NeuroPred - Tools to Predict Neuropeptides
- newDNA-Prot - DNA Binding Protein Predict Software
- newDNA-Prot 201409 - DNA Binding Protein Predict Software
- NGlycPred - N-linked Glycosylation Prediction Server Incorporating Structural Information and Patterns
- nHLAPred - Neural Network based MHC Class-I Binding Peptide Prediction Server
- NIAS-Server 1.0 - Neighbors Influence of Amino acids and Secondary Structures in Proteins
- NIEluter - Natural Immunopeptidome Eluter
- NIpredict - Nuclear Import Activity Predictor based on NLS-import Receptor Interaction
- NLR-parser 1.0 - Annotation Pipeline for NLR Genes
- NLStradamus 1.8 - Hidden Markov Model for Nuclear Localization Signal Prediction
- NNAlign 2.1 - Discovering Sequence Motifs in Quantitative Peptide data
- NNcon 1.0 – Protein Contact Map Prediction Using Artificial Neural Networks
- NoD 1.3 - Nucleolar Localization Sequences Detection
- NORINE / MyNorine - Nonribosomal Peptides Database & Tools for their Analysis
- NovoHMM - hidden Markov model for de novo Peptide Sequencing
- NOXclass - Prediction of Protein-protein Interaction Types
- NpPred - Prediction of Nuclear Proteins
- NPS@ 2016 - Interactive Web server dedicated to Protein Sequence Analysis
- NQ-Flipper 2.7 - Validate Asparagine and Glutamine Side-chain Amide Rotamers in Protein Structures
- NR-2L - A two-level predictor for Nuclear Receptor Subfamilies based on Sequence-derived Features
- NRfamPred - Webserver for Nuclear Receptor Proteins and their Sub-family Prediction
- NRpred - SVM based method for Prediction of Nuclear Receptors
- NRPSpredictor2 20111113 - Predict NRPS Adenylation Domain Specificity
- NsitePred - Prediction of Nucleotide-binding Residues
- NTXpred - Prediction of Neurotoxins from their Function and Source
- Nuc-PLoc - Predicting Protein Subnuclear Localization
- NucImport v2 - Nuclear Protein Import and Localisation Signals Predictor
- Nucleos - Identification of Nucleotide-binding sites based on the concept of Nucleotide Modularity
- NucPred 1.1 - Predicting Nuclear Localization of Proteins
- NYCE - Predict Subcellular Location of Eukaryotic Proteins based on Sequence
- OCTOPUS / SPOCTOPUS - Prediction of Membrane Protein Topology and Signal Peptides
- ORDER_AVE - Improving Orientation-dependent Statistical Potential using Reference State
- ORION - Profile-profile Fold Recognition
- orthoFind - Obtain Orthologs and Paralogs of Protein Sequence
- OSCAR - Protein Side Chain Modeling
- OSML - Predicting Protein-Ligand Binding Sites
- OSPREY 3.2.289 / gOSPREY - Computational Structure-based Protein Design / for GPU
- Oxypred - Prediction of Oxygen Binding Proteins
- P-Binder - Predicting the Binding Sites on pair of given Proteins
- P.R.E.S.S. 2.0 - Exploring Residual-level Protein Structural Statistics
- P3Fold - Predicting Protein Folding Routes
- PAAT 1.1 - Peptide Abundance Analysis Toolbox
- PAComplex - Infer Peptide Antigen Family and TCR-pMHC Binding Model
- Pafig 1.0 - Prediction of Amyloid Fibril-forming Segments
- Paircoil2 - Predict Coiled-coil Domains in Protein Sequences
- PAIRPred 1.0 - Partner Aware Interacting Residue PREDictor
- PairwiseStatSig 20110801 - Pairwise Statistical Significance
- PalmPred - An SVM Based Method for Palmitoylated Peptide Prediction
- PALSSE 20090521 - Predictive Assignment of Linear Secondary Structure Elements
- PANDA - Protein Function Prediction Using Domain Architecture and Affinity Propagation on the GO Graph
- Pandora 4.2 - Protein ANnotation Diagram ORiented Analysis
- PANNZER2 - Protein Functional Annotation Server
- pantherScore 1.03 - PANTHER HMM Scoring tool
- Paratome 1.0 - Identification of Antigen Binding Regions
- PARE - Compare Protein Abundance and mRNA Expression data
- Parepro 1.0 - Identify which nsSNP have a deleterious effect on Protein Function
- partiFold - Transmembrane Beta-barrel Proteins Predictor
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