Protein
- BASILISK 0.1 – Probabilistic Model of Side Chains in Proteins
- CellOrganizer 1.9.0 – Image-derived Models of Subcellular Organization and Protein Distribution
- Plasmo2D 1.0 – Aid Identification of Proteins from Plasmodium Falciparum
- RAPSearch 2.10 – Fast Protein Similarity Search
- HHsearch 2.0.16 – Protein Homology Detection by HMM–HMM Comparison
- PDBjViewer 4.3.1 – Display 3D Molecular Graphics of Proteins and Nucleic Acids
- CMView 1.1.1 – Protein Contact Map Visualization and Analysis
- FMA 0901 – Protein Functional Mode Analysis
- iRefIndex 10 / iRefScape 1.1.8 / iRefR 1.00 – Downloading Consolidated Protein Interaction data and Visualization
- SequenceAssembly 20111004 – Assemble Amino Acid Sequences of Entire Proteins
- SHARPEN 1.5.1 – Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network
- PhosSNP 2.0 – Influence of Protein Phosphorylation by nsSNP
- DOG 2.0.1 – Protein Domain Structure Visualization
- NetSurfP 1.0b – Protein Surface Accessibility & Secondary Structure Predictions
- ProtTest 3.2.2 – Selection of Best-fit Models of Protein Evolution
- CSM – Funciton Prediction and Fold Recognition by Protein inter-residue Distance Patterns
- ProNOI – Protein Nano-Object Integrator
- Validate Fasta File 2.1.4808 – Parse Fasta file and return the number of proteins and number of Residues
- Protemot – Prediction of Protein Binding sites with automatically extracted Geometrical Templates
- PreDNA 1.0 – Accurate Prediction of DNA-binding sites in Proteins
- StatAlign 2.1 – Bayesian Analysis of Protein, DNA and RNA Sequences
- Predikin – Predict Substrate Specificity of Protein Kinases
- iMembrane – Homology-Based Insertion of Proteins into the Membrane
- SPEPLip – Predictor of Signal Peptide and Lipoprotein Cleavage Sites in Proteins
- CCHMMPROF – Predictor of Coiled-Coils Regions in Proteins Exploiting Evolutionary Information
- AVID – Discover Functional Relationships among Proteins
- CTX-PSI-BLAST 1.0 / CTX-BLAST 1.0 – Context Sensitive version of Protein BLAST
- Papia – Protein Information Analysis System
- JOY 5.0 – Protein Sequence-Structure Representation and Analysis
- 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
- SubMito 1.1 – Predict Protein Submitochondria Locations from Sequence
- DNA/RNA/Protein and General Molecular Weight Calculator 1.0
- BRAGI 20091106 – A Protein Visualization and Modeling Program
- LFM-Pro – Detection of Significant Local Structural Sites in Proteins
- DNAbinder – Prediction of DNA-binding Proteins
- CUPSAT – Protein Stability Analysis Tool
- SCPRED – Prediction of Stabilization Centers in Proteins
- DNAbind – DNA Binding Protein prediction
- SCide – Identification of Stabilization Centers in Proteins
- SRide – Identification of Stabilizing Residues in proteins
- refolding 0.1 – Tools for Protein Unfolding and Refolding under the AFM
- metaPocket 2.0 – Meta approach for Protein Ligand-binding sites Prediction
- SurpResi 201108 – Protein Active Site Prediction based on Central Distances of Amino Acids
- SPIDER – Scoring Protein Interaction Decoys using Exposed Residues
- LACS – Validate Protein NMR Chemical Shifts
- X!TandemPipeline 3.3.0 – Peptide / Protein Identifications from MS/MS Mass Spectra
- SAMP – Structural Annotation of Malaria proteins
- SVM-FOLD – Web Tool for Protein Structural Classification
- ConSurf 2010 – Identification of Functional Regions in Proteins
- LGEpred – Correlation Analysis and Prediction of Genes Expression from Amino Acid Sequence of Proteins
- 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
- BetaTPred – Predict Beta Turns in Proteins using Existing Statistical methods
- 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
- APSSP2 – Advanced Protein Secondary Structure Prediction Server
- UNFOLD – Protein Folding Pathways
- PSIST – Protein Indexing
- GNAT 1.22 – Gene / Protein Named Entity Recognition and Normalization software
- LnLCorr – Detect Pairwise Coevolutionary among Residues in a set of Proteins
- Hipsec 1.0 – Predict High-level Protein Production in Aspergillus Niger
- iMolview 1.6 – iPhone, iPad and Android App for Browsing Protein, DNA & Drug Molecules in 3D
- pClust 1.0 – Parallel Identification of Dense Protein Clusters
- MOLARIS 9.11 – Tool for the study of Energetics and Dynamics of Protein
- ProtMod – Protein Modeling Server
- XtalPred – Prediction of Protein Crystallizability
- GraphiteLifeExplorer 20120731 – Model in 3D Assemblies of Proteins and DNA
- SLocX - Prediction of Protein subcellular localization using Gene Expression
- Phos3D – Prediction of Phosphorylation Sites (P-sites) in Proteins
- MassSorter 3.1 – Administrating and Analyzing data from Mass Spectrometry experiments on Proteins
- WEBnm@ 2.0 – Computation and analysis of Low-frequency Normal Modes for Proteins
- STITCH 3.1 – Search Tool for Interactions of Chemicals and proteins
- SMART 7.0 – Analysis of Protein Domain Architectures
- CRNPRED 1.1 – Predict Secondary Structures of Protein
- MetalloPred – Hierarchical Prediction of Metal Ion Binding proteins
- CalPred 1.0 – Calcium Binding Protein Predictor
- BRS-nonint – Balanced Random Sampling of Non-interactions between Proteins
- Moara 1.0.6 – Extract & Normalize Gene and Protein Mentions
- PIANA 1.47 – Protein Interactions And Network Analysis tool
- SNPs&GO – Predictor of Human Disease-related Mutations in Proteins with Functional Annotations
- FT-COMAR – Fault Tolerance Reconstruction of 3D Structure from Protein Contact Maps
- DCON – Predictor of Disulfide Connectivity in Proteins
- CORNET – Predictor of Residue Contacts in Proteins
- CCHMM – Predictor of Coiled-Coils Regions in Proteins
- BaCelLo – Predictor for the Subcellular Localization of Proteins in Eukaryotes
- PMUT – Web-based Tool for the Annotation of Pathological Mutations on Proteins
- ScrewFit 1.0.1beta – Characterization of Protein Secondary Structures
- GPMAW 9.21 – Mass Spectrometric Analysis of Proteins and Peptides
- PSSpred v2 – Multiple Neural Network Training program for Protein Secondary Strucure Prediction
- SAS-Pro 201106 – Sequential and Non-sequential Structure Alignment of Proteins
- HELANAL-Plus – Characterize the Geometries of Helices present in Proteins
- NRProF – Protein Function Prediction Based on the Neural Response Algorithm
- SEMPPR 1.0.2 – Stochastic Evolutionary Model of Protein Production Rates
- Rosetta 3.4 – Simulation and Design of Protein
- ProteinCCD – Protein Crystallographic Construct Design
- SVMcon 1.0 – Protein Contact Map Prediction using Support Vector Machine
- MSACompro 1.2.0 – Protein Multiple Sequence Alignment using predicted Secondary Structure
- APOLLO – Assess Protein Single or Multiple Model(s)
- NNcon 1.0 – Protein Contact Map Prediction Using Artificial Neural Networks
- PAR-3D 1.1 – Detect Protein Active site Residues using 3-Dimensional Structural Motifs
- CPLA 1.0 – Integrated Database of Protein Lysine Acetylation
- GenePro 2.5.2 – Visualization and Analysis of Protein and Gene Interaction Networks
- ProCAIn – Protein profile Comparison with Assisting Information
- VASCo 1.0.2 – Computation and Visualization of Annotated Protein Surface Contacts
- MASPECTRAS 2.3 – Integrate MS protein Identification
- PTRStalker – Protein Tandem Repeats Discovery and Visualization
- BLAT 35 – Rapid mRNA/DNA & Cross-species Protein Alignments
- PatScan – Locate Patterns in DNA or Protein FASTA files
- BiasViz 2 – Protein Amino Acid Bias Analysis Applet
- SHIFTX2 1.07 – Improved Protein Chemical Shift Prediction
- Raster3D 3.0-2 – Generate High Quality Raster Images of Proteins or other Molecules
- Hollow 1.2 – Illustration software for Proteins
- LocTree2 – Protein Sub-cellular Localization Prediction for all domains of life
- ConTest 1.0.2 – Test Constraints in Proteins
- STRAP 1.1 – Software Tool for Rapid Annotation of Proteins
- Samo 0.4.1 – Protein Structure Alignment tool based on Multiple Objective Optimization
- SANA – Protein Structure Alignment by Neighborhood Alignment
- SABIC – Protein Structure Alignment Based on Internal Coordinates
- PSN – Protein Pocket Similarity Networks
- PIPSA 3.0 – Protein Interaction Property Similarity Analysis
- POPS* 1.5.3 – Fast and Accurate Computation of Surface Areas of Proteins and Nucleic Acids
- ANAT 20111212 – Inference and Analysis of Functional Networks of Proteins
- Cytoprophet 1.0 – A Cytoscape plug-in for Protein and Domain Interaction Networks Inference
- GOSSIP – Global Structural Superposition of Proteins
- Fr-TM-align 201106 – Protein Structural Alignment
- Censor 4.2.28 – Compares and Masks Protein or Nucleotide Sequences
- DPD – Identification and Quantification of the Protein
- PSIPRED 3.3 – Accurate Protein Secondary Structure Prediction
- COILS 2.2 – Prediction of Coiled Coil Regions in Proteins
- SIMULATOR 1.0 – Simulate DNA and Protein datasets with well-defined Insertion-deletion dynamics
- Philius – Predict Protein Transmembrane Topology and Signal Peptides
- NUCPLOT 1.1.4 – Generate Schematic Diagrams of Protein-nucleic Acid Interactions
- PICR – Protein Identifier Cross-Reference Service
- DPS 2.13 – Processing of Single Crystal X-ray Diffraction data of proteins etc
- PASTA 1.0 – Protein Aggregation Prediction
- SIDEpro 1.0 – Prediction of Protein side-chain Conformations
- BETApro 1.0 – Protein Beta Sheet Predictor
- DIpro 2.0 – Protein Disulfide Bond Prediction
- MAPP 20050628 – Multivariate Analysis of Protein Polymorphism
- MORPH – Predict Protein Interaction Partners between members of two Protein Families
- Cubic 2.0.4 / JCubic 1.1 – Protein Binding Site Prediction
- MUPRED – Protein Secondary Structure Prediction
- SCOOP 0.02 – Comparison of Families of Proteins
- ViTO 20031125 – Protein Sequence Structure Alignments
- SIMPA 96 – Predict Secondary Structure of Proteins
- ESAP 4 – Predict Loop Conformation in Proteins
- IsotopeCalculator 2 – Compute Isotopic Distributions for Large Proteins
- TargetP 1.1b – Predict Protein Subcellular Localisation
- UbPred – Determine whether a Lysine Residue in a protein is ubiquitinate
- GoCore 5.0.1 – Protein Sequence Alignment and Analysis
- BioMyn – Mining Gene and Protein Knowledge
- NW-align – Protein Sequence-sequence Alignments
- MM-align 20090930 – Protein Complex Structural Alignment
- BSpred – Predict Binding Site of Proteins
- SVMSEQ 1.0 – Protein Contact Prediction
- DisEMBL 1.5 – Protein Disorder Prediction
- APAT 1.4.1 – Automated Protein Annotation Tool
- AVP 1.3 – Calculate Protein Void Volumes and Packing Quality
- ProFit 3.1 – Protein Least Squares Fitting
- IUPred – Predict Intrinsically Unstructured Regions of proteins
- Anchor – Predict Binding Regions in Proteins
- HMMTOP 2.9 – Predict Transmembrane Helices and Topology of Proteins
- NucImport – Nuclear Protein Import and Localisation Signals Predictor
- MultiLoc2 20091026 – Predict Animal, Plant and Fungal Protein Subcellular Localization
- Discriminative HMMs – Find Discriminative Motif to Predict Protein Subcellular Localization
- LoopTK 2.0.1 – Protein Loop Kinematic Toolkit
- AlloPathFinder 1.1 – Compute Likely Allosteric Pathways in Proteins
- SMAP 2.0 – Comparison & Similarity Search of Protein Three-dimensional Motif
- DEPTH 2.8.7 – Measure Extent of Atom/Residue Burial within Protein
- tCONCOORD 1.0 – Predict Protein Conformational Flexibility
- SnS-Align – Alignment of Distantly related Proteins
- DensityFit 1.0 – Analysis of Electronic Density Map for Protein
- DomainFinder 2.0.4 – Determine Dynamical Domains in Protein
- BioSeqAnalyzer 1.0 – Analyze DNA and Protein Sequences
- Genamics Expression 1.1 – DNA and Protein Sequence Analysis
- CDTree 3.1 – Protein Domain Hierarchy Viewer and Editor
- ProTag 1.4 – Office Add-In for offering SmartTag of Protein
- PAT 0.9 – Protein Alignment Tool
- DISCO 1.0 – Structure Determination of Protein Homo-oligomers
- PSAAM – Protein Sequence Analysis And Modelling
- Utopia 1.4.5 – Protein Analysis Suite
- ProtBuD – Protein Biological Unit Database
- MolIDE 1.7 – Protein 3D Homology Modeling
- SCWRL 4.0 – Prediction of Protein Side-chain Conformation
- Translate.wdgt – DNA/Protein Conversions
- I-sites 2 – Predict the Local Structure of a Protein
- HMMSTR-CM – Protein Contact Map Prediction
- HMMSTR 20091212 – Protein Secondary Structure Prediction
- ProSplign 20070709 – Alignment of Proteins against Genomic Sequences
- Bio2MIDI 2.1 – Convert DNA or Protein Sequence to MIDI file
- PREFAB 4.0 – Protein Reference Alignment Database
- Jali 1.3 – Remote Homology Detection for Protein
- lrrr 1.4 beta1 – Determines Ligands on the Surface of Proteins
- REPRO – Protein Repeats Analysis
- FiltRest3D – Filtering Protein Models by Fuzzy Restraints
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