Posts
- Category: Protein Sequence Analysis (continued)
- PASTA 2.0 - Protein Aggregation Prediction
- Patch-Surfer 2.0 / PL-PatchSurfer2 - Prediction of Binding Ligand for a Protein
- PatchD - Regional Covariation for Predicting Protein Contact Patches
- PatchFinder - Identification of Functional Regions in Proteins
- Pcleavage - SVM based 20S Proteasomal Prediction Method
- Pclust - Visualization of Protein Cluster in a Protein Similarity Network
- PCOILS 1.0.1 - New COILS version that uses Profiles as inputs
- Pcons - Protein Structure Prediction Meta Server
- PconsC - Combination of Direct Information methods and Alignments improves Contact Prediction
- PconsFold v1.0 - Pipeline for Protein Folding using PconsC and Rosetta
- PCP 1.0 - Protein Complex Prediction
- PCRPi-W - Predicting Critical Residues in Protein Interfaces
- PCSS - Peptide Classification using Sequence and Structure
- PCTpred - PTM Cross-Talk predictor
- PDART - Protein Domain Architecture Retrieval Tool
- PDEXK - Server for Detection of new Protein Families from the PD-(D/E)XK Superfamily
- PDZPepInt 1.0.0 - PDZ-peptide Interaction prediction
- PEASE - Predicting Epitopes using Antibody Sequence
- PEAT / PEATDB 2.3 / PEATSA - Protein Engineering Analysis Tool
- PEIMAN - Enrichment Analysis in Post Translational Modification (PTM) types
- PEP-SiteFinder - Identify Candidate Protein-peptide Interaction Sites.
- PepExplorer 0.1.0.78 - Statistically Filtering and Organising de novo Sequencing Results
- PepFly - Peptide Flyability Prediction
- PepNovo 20120423 - De novo Sequencing of low Precision MS/MS Data
- PepSite 2 - Prediction of Peptide Binding Sites on Protein Surfaces
- PEPstrMOD - Peptide Tertiary Structure Prediction with Natural, Non-natural Modified Residues
- PeptideLocator - Identifies Bioactive Peptides in Protein Sequences
- Peptidequant - Optimization-based Peptide Quantification tool
- Peptides 2.6 - Peptide and Protein Physico-chemical Properties
- Peptizer 1.8.4 - Automating manual Validation of MS/MS Search results
- Periscope 20150806 - A Predictor for Soluble Protein Expression in the Periplasm of Escherichia coli
- PETs 0.9 - Predictor of Protein-Protein Interaction Sites based on Extremely-randomized Trees
- PexSPAM 1.2 - Protein Sequence Feature Extraction
- Pfam 32.0 - A database of Protein Domain Families
- pfilt 1.5 - Sequence Filtering for Low-complexity, Coiled-coil and Biased Amino Acid Regions
- pFlexAna 0.1.1 - Protein Flexibility Analyzer
- PFMpred - Predicting Mitochondrial Proteins of P.falciparum
- PFP / ESG - Sequence Similarity-based Protein Function Prediction server
- PFP 2.3 - Extracting and Displaying Positive Electrostatic Patches on Protein Surfaces
- PFP-FunDSeqE - Predicting Protein Fold Pattern
- PFP-Pred 2.0 - Protein Fold Prediction
- PFSTATS 0.98 - Analyze Protein Families using simple Statistics
- pGenTHREADER 8.9 - Protein Fold Recognition by Profile-profile Threading
- Philius - Predict Protein Transmembrane Topology and Signal Peptides
- Phobius /PolyPhobius 1.05 - Combined Transmembrane Topology & Signal Peptide Predictor
- Phogly-PseAAC - Prediction of Lysine Phosphoglycerylation in Proteins
- Phos3D - Prediction of Phosphorylation Sites (P-sites) in Proteins
- PHOSFER - PHOsphorylation Site FindER
- Phosfinder - Phosphate Binding Sites prediction on Protein Structures
- PhosNetConstruct - Phosphorylation Network Reconstruction
- PhosPatch - Phosphorylation Site Patch Analysis
- Phospho.ELM 9.0 - Database of Phosphorylation Sites
- PhosphoPICK - Phosphorylation in a Protein Interaction Context for Kinases
- PhosphoRice 1.1.1 - Meta-predictor of Rice-specific Phosphorylation Site
- PhosphOrtholog - Cross-species Mapping of Orthologous Protein Post-translational Modification
- PhosphoSitePlus - Tools for the study of Protein Post-translational Modifications
- PhosphoSVM - Non-kinase-specific Phosphorylation site Prediction tool
- PhosSNP 1.0 - Influence of Protein Phosphorylation by nsSNP
- PhosTryp - Phosphorylation Site prediction in Trypanosomatidae
- PHOXTRACK - PHOsphosite-X-TRacing Analysis of Causal Kinases
- PHPred - A sequence-based tool for Identifying Phage Proteins located in Host Cell
- PhyloHMM v2 - Proteome-wide Discovery of Evolutionary Conserved Sequences in Disordered regions
- PHYPred - Identifying Phage Enzymes and Hydrolases
- PHYSICO 2 - Computation of Properties of Protein Sequences
- PhysMPrePro 1.0 - Recognizing Prokaryotic Promoters based on Molecular Structure
- PICR - Protein Identifier Cross-Reference Service
- PIE 0.35 / PIE-Web - Protein Inference Engine
- PIP - webserver for Potential Protein-protein Interactions
- Pipasic 20140121 - Protein Abundance Correction in Metaproteomic Data
- PIPS 1.0 - Phylogenetic Inference of Protein Stability
- PIPs 1.1 - Human Protein-Protein Interaction Predictions
- PISCES 20210711 - Protein Sequence Culling Server
- PIUS 1.0 - Peptide Identification by Unbiased Search
- PIVOT 2.0 - Protein Interactions VisualizatiOn Tool
- pKaTool - Analyse Protein pKa Calculations and play with Titratable groups
- PL-search V1 - A profile link based search method for protein remote homology detection
- PLAAC - Prion-Like Amino Acid Composition
- PlantTFcat - Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool
- PlifePred - Design Half-life of Peptides in Blood
- PMB matrix - Data file to use with Ziheng Yang's PAML for Protein Sequence Analysis.
- PMUT - Web-based Tool for the Annotation of Pathological Mutations on Proteins
- PocketAlign - Aligning Binding Sites in Protein Structures
- PocketDepth - A new depth based algortihm for Identification of Ligand Binding Sites
- PocketMatch 2.1 - Compare a pair of Binding Sites
- POLYVIEW-2D / POLYVIEW-3D / POLYVIEW-MM - Protein Structure Annotation using Sequence Profiles / Structures / Motions
- PoreLogo 1.0 - analyse, visualize and compare channels in Transmembrane Proteins
- PoreWalker - Detecting Transmembrane Protein Channels from their 3D Structure
- Porter, PaleAle 4.0 - Prediction of Protein Secondary Structure and relative Solvent Accessibility
- PoSSuM / PoSSuMsearch 2.0 - Matching of PPSSMs using Enhanced Suffix Arrays
- POW - PDZ Domain-peptide Interaction Prediction
- PPA-Pred 2 - Protein-Protein Affinity Predictor
- PPCMatrix 1.25 - Dotmatrix program to Compare large Genomic Sequences against Protein Sequences
- PPCpred - Crystallization, Purification, and Production Propensity Prediction
- PPI / PPI_RF - Prediction of Protein-Protein Interactions
- PPI-PS - Protein-protein Interaction based on Pairwise Similarity
- PPIP - Protein-Protein Interaction Predictor
- PPMs / PPMs-sl / PPMs-mcsl / PPMs-sub - Protein 3D Similar Substructure
- Pprint - Prediction of Protein RNA- Interaction
- PPS - Find Palindromes in all Protein Sequences
- PPS 1.0 - PTMs Peptide Scanner
- PPSP 1.06 - Prediction of PK-Specific Phosphorylation Site
- Pratt 2.1 - Find Flexible Patterns in Unaligned Protein Sequences
- PREAL - Prediction of Allergenic Protein
- Pred_enzyme 1.0 - Prediction of Acidic and Alkline enzyme
- PRED-SIGNAL - Prediction of Signal Peptides in Archaea.
- PRED-TMBB - Predicting and discriminating beta-barrel outer membrane proteins with Hidden Markov Models
- PREDAC-H3 20200907 - Bioinformatics platform for Antigenic Surveillance of human Influenza H3N2 Virus
- PredAlgo 1.0 - Protein Subcellular Localization Prediction in Green Algae
- PreDBA 1.1 - Prediction of Protein-DNA Binding Affinity
- PredBF - Robust Prediction of B-factor Profile from Sequence
- PredCSF - Predicting Conotoxin Superfamily
- PREDDIMER - Prediction tool for an Ensemble of Transmembrane α-helical Dimer Conformations
- PredGPI - Predictor of GPI-Anchored Proteins
- PredHS 1.0.5 - Prediction of Hot Spots by Using Structural Neighborhood Properties
- PredictFold-PSS-3D1D - Protein Fold Recognition Web Server
- PredictProtein 1.1.10 - Protein Sequence Analysis, Prediction of Structural and Functional Features
- PredictSNP2 - Unified Platform for Prediction of SNP effect in Distinct Genomic Regions
- Predikin - Predict Substrate Specificity of Protein Kinases
- PrediSi - Predict Signal Peptide Sequences
- PREDITOR - Predicting Torsion Angles in Proteins from NMR Chemical Shifts and/or Homology
- PREDIVAC - CD4+ T-cell Epitope Prediction for Vaccine Design
- PreDNA 1.0 - Accurate Prediction of DNA-binding sites in Proteins
- PredUs 1.2.0 - Prediction of Protein Interfaces Using Structural Alignment
- PredyFlexy - Flexibility and Local Structure prediction from sequence
- Prelude & Fugue - Predicting local Protein Structure, early Folding Regions and Structural Weaknesses
- PreMieR - Prediction of Mannose Interacting Residue
- PreMoTF 20121109 - Homeodomain Specificity Predictions
- PrePPI - Predicting Protein-Protein Interactions by Combining Structural and non-Structural Information
- PresCont - Predicting Protein-protein Interfaces
- Presep 1.0 - Predicting the Propensity of a Protein being secreted into the Supernatant when Expressed in Pichia pastoris
- Prethermut 3.1 - Predicting Changes in Protein Thermostability brought about by Single- or Multi-site Mutations
- PreTP-EL - Prediction of Therapeutic Peptides based on Ensemble Learning
- PRince - Structural and Physicochemical analysis of Protein-RNA Interface
- PrISE 20110723 - Prediction of protein-protein Interface residues using Structural Elements
- PrISM - Protein Informatics System for Modeling
- Pro-BS - Predicting the Binding Sites for the given Proteins
- ProACT 2 - Analysis of Protein Accessibilities, Cavities and Contacts
- ProBias/BIAS - Detect Compositional Bias in Biological Sequences
- ProCAIn - Protein profile Comparison with Assisting Information
- PROCHECK 3.5.4 - Check Stereochemical Quality of Protein Structures
- PROCLASS - Protein Structure Classification Server
- PrOCoil 2.14.0 - Predicting the Oligomerization of Coiled Coil Proteins
- ProCon 2.0 - Localization & Visualization of Protein Conservation
- ProCope 1.2 - Protein Complex Prediction and Evaluation
- ProDec-BLSTM - Protein Remote Homology Detection based on Bidirectional Long Short-Term Memory
- Prodepth - Predict Residue Depth from Protein Sequences only
- ProDGe 20110509 - Investigate Protein-protein Interactions at the Domain level
- Prof 1.0 - Secondary Structure Prediction System
- prof_sim - Profile-profile Comparison Algorithm
- PROFEAT 2016 - Protein Feature Server
- ProFET 1.0 - Protein Feature Engineering Toolkit
- ProFunc - Predicting Protein Function from 3D Structure
- ProInflam - Prediction of Proinflamatory Epitopes
- ProMK - Predicting Protein Function using Multiple Kernels
- PROMPT 0.9.7 - Protein Mapping and Comparison Tool
- ProP 1.0c - Arginine & Lysine propeptide Cleavage Sites in Eukaryotic Protein
- ProPAS 1.1 - Protein Property Analysis Software
- ProPred1 / ProPred - Predict MHC Class-I / Class-II Binding Regions in Antigen Sequence
- ProQ2 / ProQM - Membrane Protein / Protein Quality Predictor
- PRORATE - Prediction of Protein Folding Rates
- ProSAT - PROtein reSidue Annotation Toolkit
- ProSAT+ - Protein Structure Annotation Tool
- PROSE 0.02a - Prosite Pattern search
- ProSpect 0.3.6 - Processing of SELDI Protein Spectra
- PROSPECT 2.0 - Threading-based Protein Structure Prediction System
- PROSPER - Protease Substrate Specificity Webserver
- PROSTA-inter 20141229 - PROtein STructure Alignment tools
- Protael 1.1.0 - JavaScript Library for Visualizing Biological Sequences and related data
- ProTag 1.4 - Office Add-In for offering SmartTag of Protein
- ProtDCal 4.5 - Computing Multiple Numerical Descriptors for Protein Sequences and Structures
- ProtDec-LTR 3.0 - Application of Learning to Rank to Protein Remote Homology detection
- ProtDet-CCH - Protein Remote Homology Detection by combining Long Short-Term Memory and Ranking methods
- PROTEAN - Torsion Space Molecular Simulations
- Protein Cavity Search 0.21 - Identify Cavities and Crevices in Proteins
- Protein Coverage Summarizer 1.3.7993 - Determine Percent of Residues in Protein Sequence
- Protein Digestion Simulator 2.2.6794 - Read a Text file containing Protein sequences and output the data to a Tab-delimited file
- Protein Peeling 3D - Splitting Protein Structure into Proteins Units and Domains
- Protein Prowler 1.2 - Subcellular Localisation Predictor
- Protein Sequence Motif Extractor 1.0.4752 - Look for the specified Motif in each Protein Sequence
- ProteinCCD - Protein Crystallographic Construct Design
- ProteinEvaluator 1.0.0 - Protein Sequence Prediction Evaluator
- ProteinEvolverABC - Estimation of Recombination and Substitution Rates in Alignments of Protein Sequences
- ProteinFuncPred - Protein function prediction
- ProteinLasso - Lasso Regression Approach to Protein Inference problem
- Proteinortho 6.30 - Orthology Detection Tool
- ProteinPathTracker - Find Orthologs Selected to study the Evolutionary Path of Protein
- ProteinVis 2.1.6 - Tree viewer for Hierarchical Clusterings of Proteins
- ProteinVolume 1.3 - Calculating Molecular van der Waals and Void Volumes in Proteins
- Protemot - Prediction of Protein Binding sites with automatically extracted Geometrical Templates
- Proteny 0.1 - Analyze Synteny at the Protein Level
- Proteomatic 1.2.1 - Platform for creating MS/MS data Analysis Workflows using Scripts
- ProteoVision - Advanced Visualization of (Ribosomal) Proteins
- PROTEUS 2.0 - Universal Protein Structure Prediction Server
- ProtFold-DFG V1 - Protein Fold recognition by combining Directed Fusion Graph and PageRank algorithm
- ProtIdent - Identifying Proteases and their Types
- PROTMAP2D 1.2.2 - Calculation, Visualization & Comparison of Contact Map
- Protomata learner - Complex Pattern Discovery based on Grammatical Inference
- protpy 1.0 - Development of Protein Descriptors using Python
- ProtQuant - Tool for Label-free Protein Quantification
- protr 1.6-2 / ProtrWeb - Generating Various Numerical Representation Schemes of Protein Sequence
- ProtRe-CN - Protein Remote Homology Detection
- PROVEAN 1.1.5 - Protein Variation Effect Analyzer
- ps_scan 1.87 - PROSITE scanning program
- PS-COILS 1.0 - Coiled-coil Predictor
- PS-HomPPI v1.3 / NPS-HomPPI - Protein-Protein Binding Site Predictor
- PSAAM - Protein Sequence Analysis And Modelling
- PseAAC - Generating Pseudo Amino Acid Composition
- PseAAC / PseAAC-Builder 3.0 / PseAAC-General - Generating Pseudo Amino Acid Composition
- PSFM-DBT - Identifying DNA-binding Proteins
- PSI-predictor - Plant Subcellular Localization Prediction
- PSICOV 2.40 - Accurate Contact Prediction from Large Protein Alignments
- PSIPRED 4.02 - Accurate Protein Secondary Structure Prediction
- PSIST - Protein Indexing
- PSIVER - Prediction of Protein-protein Interaction Sites in Protein Sequences
- PSLpred - SVM based method for the Subcellular Localization of Prokaryotic Proteins
- PSOPIA 20130501 - Prediction Server of Protein-Protein Interactions
- PSORTb 3.0.3 / PSORT / PSORT II /WoLF PSORT 0.2 - Prediction of Protein Localization sites for Bacterial Sequences / Eukaryotic Sequences/ Plant Sequences
- PSP - Prediction of Structural Aspects of Protein Residues
- PSpro 2.0 - Predict Secondary Structure, Solvent Accessibility, and Residue-residue Contacts
- PSS 1.2 / PSSweb - Protein Structural Statistics
- PSSM-DT - Identifying DNA-binding proteins by combining Support Vector Machine and PSSM Distance Transformation
- PSSpred v2 - Multiple Neural Network Training program for Protein Secondary Strucure Prediction
- pSuc-Lys - Predict Lysine Succinylation sites in Proteins with PseAAC and Ensemble Random Forest Approach
- PSVS 1.5 - Protein Structure Validation Software Suite
- PTGLtools - Visualization of Protein-Ligand Graphs software package
- PTMClust 1.1 - A Post-translational Modification Refinement Algorithm
- PTMPred - Predict Post-transcriptional Modification sites from Protein sequences
- PTRStalker - Protein Tandem Repeats Discovery and Visualization
- PubServer - Literature Searches by Homology
- PUDGE - Protein Structure Prediction Pipeline
- PULSE - Positive Unlabeled Learning for Splicing Elucidation
- Putracer - Protein Unit Tracer
- pviz 0.1.12 - Dynamic JavaScript & SVG library for Visualization of Protein Sequence Features
- PVPred - Identification of Phage Virion Proteins
- PyMod 1.1 - Sequence Similarity Searches, Multiple Sequence-structure Alignments, and Homology Modelling within PyMOL
- PyNISTPL - Python module that Interfaces to the NIST MS Search Engine libraries
- PyRosetta 2.012 - Python-based Interface to Rosetta Molecular Modeling Suite
- QCS - Quality Control Score For Quality Assessment of Protein Structure Prediction
- QFC - Quasi-Periodic Feature Classifier algorithm for G protein-coupled receptors
- Qgrid - Identify Clusters of Charged and Hydrophobic Regions in Proteins
- QHELIX 20120813 - Analysis of Geometric Arrangement of Protein Helices
- QuasiMotiFinder v4 - Protein Annotation Using a Search for Signature Like Patterns
- Quat-2L - Predicting Protein Quaternary Structural Attributes
- QuatIdent - identifying the Quaternary Structural Attribute of a Protein Chain
- QUEEN 1.1 - Quantitative Evaluation of Experimental NMR Restraints
- R3P-Loc - Multi-Label Protein Subcellular Localization Prediction
- RADAR 1.1.5 - Rapid Automatic Detection and Alignment of Repeats in protein sequences
- Rankprop - Protein Ranking by Network Propagation
- Raphael 1.0 - Determination of Periodicity in Protein Structures
- RAPID - Regression-based Accurate Prediction of protein Intrinsic Disorder Content
- RASP 1.90 - RApid Side-chain Predictor
- rate4site 2.01 - Detect Conserved Amino-acid Site
- rBAN - retroBiosynthetic Analyisis of Nonribosomal peptides
- RBPmap 1.2 - Motifs Analysis and Prediction of RNA Binding Proteins
- RBRDetector - Prediction of Binding Residues on RNA-binding Protein Structures
- RBRIdent - Identification of RNA-binding Residues in Proteins from primary Sequences
- RCDP - Performs Co-evolutionary Analysis of Domains in Interacting Proteins to Predict Domain Pair(s)
- RCI - Predict Protein Flexibility by Calculating Random Coil Index
- RCI - Prediction of Protein Flexibility using Random Coil Index
- Rcpi 1.28.0 - Compound-Protein Interaction in Drug Discovery
- RDC-PANDA 1.0 - NMR NOE Assignment & Protein Structure Determination
- ReadOut - Calculation of Direct and Indirect Readout energy Z-scores for Protein-DNA complexes
- RefineHMM 1.0.0 - HMM Refinement software
- refolding 0.1 - Tools for Protein Unfolding and Refolding under the AFM
- REPPER - Detect Regions with Short Gapless REPeats in Protein Sequences
- REPRO - Protein Repeats Analysis
- RES - Scan Protein Sequence for its Repeatability
- ReUPRed 20160310 - Identification of Repetitive Units in Protein Structures
- RFcon - Predict Protein Residue-residue Contacts using Random Forests and Deep networks
- RFPR-IDP - Reduce the False Positive Rates for intrinsically Disordered Protein
- RFQAmodel - Identify Predicted Protein Structure in the Correct Fold
- RHYTHM 0.3 - Knowledge-based Prediction of Helix-helix Contacts
- RING v2.0.1 - Web Server for high quality Residue Interaction Networks
- RNABindRPlus 1.0 - Prediction of RNA-binding Residues in Protein
- RNAcode 0.3 - Analysis of Protein Coding Potential in Multiple Sequence Alignments
- RNApred - Prediction of RNA-binding Proteins
- RNAProt v0.4 - Modelling RBP binding preferences to predict RPB Binding Sites
- Rosetta 3.13 - Simulation and Design of Protein
- RPAIAnalyst - Exploiting Properties of Residue Pairs to Analyze Protein Interfaces
- RSARF - Prediction of Solvent Accessibility from Protein Sequence using Random Forest Method
- RSLpred - Predicting Subcellular Localization of Rice Proteins
- RSpred - Rifin/Stevor Prediction tool
- RUBI 1.0 - Rapid UBIquitination Detection
- RVP-NET 2.0 - Real Value Prediction of Solvent Accessibility
- RW 1.0 - Protein Structure Modeling and Structure Decoy Recognition
- S-PSorter - Predicting Image-based Protein Subcellular Location
- SA-Mot - Extract Structural Motifs from Protein Loop Structures using HMM-SA
- SAAB+ v1.0.0 - Structural Annotation of BCR Repertoires
- SAAFEC-SEQ - Pedict the stability Changes upon a Single Mutation in Protein
- SAAMBE - Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations
- SABINE 1.2 - Prediction of the Binding Specificity of Transcription Factors using Support Vector Regression
- SABLE v4 - Accurate sequence-based prediction of relative Solvent AccessiBiLitiEs
- Sadic / ProCoCoA 1.1b10 - Simple Atom Depth Index Calculator / Protein Core Composition Analyzer
- SALAMI - Protein Structure Alignment
- Sann - Solvent Accessibility Prediction by Nearest Neighbor Method
- SANS / SANSparallel 2.3 - Interactive Homology Search against Uniprot
- sapFinder 1.26.0 - Detection of Variant Peptides in Shotgun Proteomics Experiments
- SAPTF 1.7 - Sequence Analysis Plugin Tool Framework
- SARA 1.0 - Side-chain Angular Replacement Algorithm
- SAROTUP 3.1 - Target-Unrelated Peptides Scanners
- SARpred - Prediction of real value of Surface Accessibility in proteins from Amino Acid Sequence
- SAS - Sequence Annotated by Structure
- SBSPKS - Structure Based Sequence Analysis of Polyketide Synthases
- SCALOP - Sequence-based antibody CAnonical LOoP structure annotation
- SCAMPI2 - Improved Topology Predictions using the First and last Hydrophobic Helix Rule
- scan-x 1.1 - Find Motifs within any Sequence data set
- ScanSite 4.0 - Kinase-substrate Interaction Prediction and Short Linear Sequence Motif Discover
- SCide - Identification of Stabilization Centers in Proteins
- SCLpredT - Protein Subcellular Localization Prediction
- SCooP 1.0 - Prediction of the Stability Curve of Proteins
- Scorecons - Score Residue Conservation in a Multiple Sequence Alignment
- SCORER 2.0 - Distinguish Parallel Dimeric and Trimeric Coiled-coil Sequences
- SCPRED - Prediction of Stabilization Centers in Proteins
- ScrewFit 1.0.4 - Characterization of Protein Secondary Structures
- SCWRL 4.0 - Prediction of Protein Side-chain Conformation
- SECISearch3 and Seblastian - Prediction of SECIS Elements and Selenoproteins
- SECOM 1.0 - Genome-scale Protein Domain Identification
- SecretomeP 2.0 - Prediction of Non-classical Protein Secretion
- Seder 2.0 - A Global Protein Structure Scoring Function
- SEGMER - Protein Substructure Recognition
- Selecton 2.4 - Identification of Site-Specific Positive Selection & Purifying Selection
- SELECTpro 1.0 - Protein Model Scoring/Selection and Side-Chain Prediction
- SemiBiomarker - Bioimage-based Semi-supervised Method for Protein Subcellular Localization
- Sephiroth 20140618 - Disulfide Connectivity Prediction
- SEPPA 3.0 - Server for Conformational B-cell Epitope Prediction
- Seq2Logo 2.1 - Sequence Logo Generator
- Seq2Ref 1.2 - Facilitate Functional Interpretation
- SeqNLS - Nuclear Localization Signal Prediction
- SeqRate 1.0 - Sequence-based Prediction of Protein Folding rates
- seqsee 1.6 - Protein Sequence Analyzer
- SequenceAssembly 20111004 - Assemble Amino Acid Sequences of Entire Proteins
- SequenceAssignCompare 20111109 - Automated MALDI-ISD Protein Sequencing Software
- SeSAW 2.0 - Functional Mapping by Sequence-Derived Structural Alignment Weights
- SH2PepInt 1.0.0 / SH3PepInt 1.0.0 - SH2-peptide / SH3-peptide Interaction Prediction
- SHARPEN 1.3 - Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network
- SherLoc2 20091026 - Predicting Protein Subcellular Localization
- Sherlocc 1.0 - Detect Statistically Relevant Conserved Rare Codon Clusters
- Shifty 1.3 - Automated Protein Chemical Shift Prediction
- SHIPREC - Salmonella/Host Protein-Protein Interaction Predictions Browser
- SIBIS 1.0 - Bayesian model for Inconsistent Protein Sequence Estimation
- SIDEpro 1.0 - Prediction of Protein side-chain Conformations
- SIFT 6.2.1 - Amino Acid Substitution Affects Protein Function
- SIFTER 2.1.1 - Genome-scale Phylogenetic Function Annotation of Protein Families
- sig 1.0 - Multiple Prosite Motifs searching
- Signal-3L 3.0 - A 3-layer Approach for Predicting Signal Peptides
- Signal-CF - Predicting Signal Peptides
- SignalP 5.0 - Predict Signal Peptides
- SigniSite 2.1 - Residue level Genotype Phenotype Correlation in Protein Multiple Sequence Alignments
- SILACtor 1.0 - Dynamic SILAC studies
- SIM 0.9.4.9 - Peptide Sequence Matching tool
- SIMPA 96 - Predict Secondary Structure of Proteins
- Simprot 1.03 - Simulate Protein Evolution
- SiTaR - Transcription Factor Binding Site Prediction
- Skyline 21.1 - Targeted Proteomics Environment
- SLIDER - High-throughput Prediction of Proteins with long Disordered Segments
- SLiMSuite v1.9.1 - Bioinformatics Tools to Analyse Protein Features
- SLPFA - Subcellular Location Prediction with Frequency and Alignment
- SMAP 2.0 - Software for Ligand Binding Site Comparison
- SMART 8.0 - Analysis of Protein Domain Architectures
- SMI-BLAST v1 - Search framework based on PSI-BLAST for protein remote homology detection
- SMOQ 1.0 - Protein Single Model Local Quality Prediction
- SMURF / SMURFLite - Simplified / Structural Motifs Detection Using Random Fields
- SNAP - Predicts Effect of Mutations on Protein Function
- SNPs&GO - Predictor of Human Disease-related Mutations in Proteins with Functional Annotations
- SOCKET 3.03 / iSocket 0.3.1 - Identifies Knobs-into-holes packing in Protein Structures
- SODa - SuperOxide Dismutase Annotation Tool
- SOLart 1.0 - Protein Solubility Prediction
- SOLpro - Prediction of Protein Solubility upon Overexpression
- SOMPNN - An Efficient Non-Parametric Model for Predicting Transmembrane Helices
- SOMRuler - A Novel Interpretable Transmembrane Helices Predictor
- SORTALLER - Predicting Allergens based on Allergen Family Featured Peptides (AFFP) algorithm
- SOV_refine - A Further Refined Definition of Segment Overlap Score
- SPANS 1.0 - Statistical Procedure for the Analyses of peptide abundance Normalization Strategies
- SpaPredictor - Interpretable Protein Subcellular Localization
- SPAR v1.0 - Predictor for self-interacting protein from Sequence Information
- SPARKS-X - Structure Prediction from Sequence
- SPEER 201010 - Prediction of Protein Specificity Determining Sites
- SPEPLip - Predictor of Signal Peptide and Lipoprotein Cleavage Sites in Proteins
- Spial - Analysis of Subtype-specific Features in multiple Sequence Alignments of Proteins
- SPICE 0.9 - Protein Sequences, Structures & Annotations Browser
- SPICKER 2.0 - Cluster Protein Structures for Near-native Model Selection
- SPIDER - Scoring Protein Interaction Decoys using Exposed Residues
- SPOCS 1.0.10 - Graph-based Ortholog/Paralog Prediction tool
- SPOT-Seq-RNA - RNA-binding Protein prediction from sequence
- SPOT-Struct-RNA - RNA-binding Protein Prediction from 3D structure
- SPOUSE - Calculating Protein Energy for Selected Chain
- SPPIDER - Solvent accessibility based Protein-Protein Interface iDEntification and Recognition
- SPPS - Sequence-based Protein Partners Search
- SPRING - Accurate Template Recognition for Protein Complex Structure
- SPRINT - Scoring PRotein INTeractions
- SPRINT 3.0 - Side-chain PRediction INference Toolbox for Multistate Protein Design
- SProtP - Recognition of Short-lived Human Proteins
- SRide - Identification of Stabilizing Residues in proteins
- SRTpred - SVM based method for Prediction of Secrteory Proteins
- SSCon - Consensus-based Secondary Structure predictor
- SSEA-OMP - Outer Membrane Protein Discrimination
- SSKDSP - Single Source K Diverse Shortest Paths Algorithm
- SSP - Secondary Structure Propensity
- SSP 1.0 - SUMO Substrates Prediction
- SSPred - Identification & Classification of Proteins involved in Bacterial Secretion Systems
- SSpro / ACCpro 5.2 - Protein Secondary Structure /Solvent Accessibility Prediction with Homology Analysis
- SST - Secondary Structural Assignment Program
- StarPDB - BLAST-based Structural Annotation of a Protein
- STEPP 1.0 - SVM Technique for Evaluating Proteotypic Peptides
- StoatyDive v1.1.0 - Evaluation and Classification of Peak Profiles for Sequencing data
- STON - Protein 3D Structure Comparison
- STORM 1.01 - Protein Analyses of BLAST, FASTA, Pfam and ProtParam
- STRIDE - Secondary Structure Assignment from known Atomic Coordinates of Proteins
- Strike - Protein-protein Interaction Classification tool
- subGolgi v2.0 - Prediction of subGolgi locations of Proteins
- SubNucPred - Web-server for Prediction of Sub-nuclear Localization of Proteins
- SUBWAI 1.0 - Protein Structure Prediction program
- SUMOsp 2.0.4 / GPS-SUMO 1.0 - SUMOylation sites Prediction
- Super 0.3 - Screen Superposable Oligopeptide Fragments from PDB
- SUPRB 1.0 - Threading Strucuture Prediction
- SurpResi 201108 - Protein Active Site Prediction based on Central Distances of Amino Acids
- SVM-PB-Pred - Protein Block (PB) prediction server
- svmPRAT 1.0 - svm-Based Protein Residue Annotation Toolkit
- SVMProt - Protein Functional Family Prediction
- SVMSEQ 1.0 - Protein Contact Prediction
- SVMTriP - prediction of Antigenic Epitopes
- T-Analyst v2 - Efficient Analysis of Protein Conformational Changes
- T3SEpre - T3S effector Prediction model based on joint features including Aac, Sse and Acc
- Tag-DB 0.4.0 - de novo Sequencing and Tag-based database Searching of MS/MS Spectra
- Tally - Scoring tool for Boundary Determination
- TANGLE - Protein Backbone Torsion Angle Prediction from Primary Sequences
- Tango 2.3.1 - Prediction of B-sheet Aggregation in unfolded Polypeptide Chains
- TAP 1.1 - Protein Structure Validation
- TAPPred - Predict Peptide TAP Binding Affinity
- TargetATP - Predicting Protein-ATP Binding Site
- TargetCrys - Protein Crystallization Predictor
- TargetDisulfide - Disulfide Connectivity Prediction with Modelled Protein 3D Structural Information and Random Forest Regression
- TargetFreeze - Protein Sequence-based AFP predictor
- TargetP 2.0 - Predict Protein Subcellular Localisation
- TargetS - Predictor for Targeting Protein-ligand Binding Sites
- TargetSOS - Supervised Over-sampling Predictor for Targeting Protein-nucleotide Binding Residues
- TargetVita - Vitamin-specific Predictor for Targeting Protein-vitamin Binding Residues
- TAXFOLD - Improve Toxonomy-based Protein Fold Recognition
- TBBpred - Transmembrane Beta Barrel prediction
- TBpred - SVM based Subcellular Localization Prediction method for Mycobacterial Proteins
- TCRBuilder - Multi-state T-cell Receptor Structure prediction
- TepiTool - Computational Prediction of T Cell Epitope Candidates
- Terminus 0.4.1 - N-Terminal PTM prediction
- TetraMito - Prediction of Submitochondria Locations of Proteins
- TFBSs 1.0 - Predicting Transcription Factor Binding Sites
- TFpredict 1.3 - Identification and Structural Characterization of Transcription Factors
- ThermoPred - Identification of Thermophilic Proteins
- ThreaDom - Predicting Protein Domain Boundary by Multiple Threading Alignment
- TIM-Finder - A TIM-barrel Fold Recognition System
- TM-score 20190822 - Calculate Similarity of Topologies of two Protein Structures
- TMDET 2.0 - Detection of Transmembrane Regions of Membrane Protein
- TMHcon 20101215 - predict Contacts for Transmembrane Proteins
- TMhhcp - Transmembrane Helix-Helix Contact Predictor
- TMHindex - Detecting Transmembrane Helix
- TMHMM 2.0c - Prediction of Transmembrane Helices in Proteins
- TMKink - Transmembrane Kink Predictor
- TMM@ - Trans-Membrane alpha-helical Movement Analyzer
- TMpred 1.0 - Prediction of Transmembrane Regions and Orientation
- Topcons 2.0 / TOPCONS-single - Consensus Prediction of Membrane Protein Topology / without BLAST runs
- TOPO2 - Create Transmembrane Proteins Images
- Topoview - Membrane Protein Topology Viewer
- toppred 1.10 - Topology Prediction of Membrane Proteins
- TOPS / Tops editor - Topology Of Protein Structure
- ToxinPred - Designing and Prediction of Toxic Peptides
- TpPred - Prediction and Classification of Transport proteins
- TPpred 3.0 - Detection of Mitochondrial-targeting Signals in Proteins
- TraceGD 1.0 - Genetic Disease Prediction tool
- TRAL 2.0 - Tandem Repeat Annotation Library
- transFold - Super-secondary Structure Prediction of Transmembrane β-barrel proteins
- TRDistiller - Tandem Repeats Detection
- TreeDet v2 - Predicting Functional Residues in Protein Sequence Alignments
- TREND - Platform for Protein Evolution and Function Analysis
- TrSSP - Transporter Substrate Specificity Prediction Server
- TRUST 1.0 - Repeat Detection Method
- TSEMA - Prediction of Protein Pairings between interacting families
- TSpred - Predict Substitutions that Transform Query Protein Sequence/structure into Temperature-sensitive Mutant
- TumorHPD - Designing of Tumor Homing Peptides
- UbPred - Determine whether a Lysine Residue in a protein is ubiquitinate
- UnderlyingFilter - Filtering Degenerate Motifs with Application to Protein Sequence Analysis
- UProC 1.2.0 - Tools for Ultra-fast Protein Sequence Classification
- VADAR 1.8 - Structural Analysis of Protein Coordinates
- Validate Fasta File 2.2.7887 - Parse Fasta file and return the number of proteins and number of Residues
- Varun - Extensible Motif Discovery
- VaxiJen 2.0 - Prediction of Protective Antigens and Subunit Vaccines
- VaxinPAD - Prediction of Immunomodulatory Peptides for use as Vaccine Adjuvants
- VDJsolver 1.0b - Analysis of Human Immunoglobulin VDJ Recombination
- VGIchan - Voltage Gated Ion Channel Prediction server
- VICMpred - Prediction of Functional Proteins of Gram-negative Bacteria using Amino Acid Patterns and Composition
- VIRALpro 1.0 - Prediction of Viral Capsid and Tail Sequences
- VitaPred - Prediction of Vitamin Interacting Residues
- VLDP - Analysing Protein Structures in their Environment
- Waggawagga - Coiled-coil and Single-Alpha-Helix prediction for Protein Sequences
- WDRR - WD40 Repeat Recognition
- WEBnm@ 3.3 - Web-server for Normal Mode Analysis of proteins
- WESA - Weighted Ensemble Solvent Accessibility
- Wise 2.4.1 - Compare Protein Sequence to Genomic DNA Sequence
- wKinMut 2 - Integrated Framework for the analysis of Kinase Mutations
- Wregex 2.1 - Amino Acid Motif searching
- Wsearch v1 - Identification of Potential AGO-binding Sites
- WURSTL 20150526 - Protein Superposition Tool
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