Chromatography lecture and my learning diaries
The chromatography is a collective terms for separation of mixtures
techniques. The sample (Mixtures) is dissolved in the mobile phase,
which carried it through the stationary phase. The separation was
achieved by the difference of travel time/speeds. Several chromatography
methods have been developed during the past time including paper
chromatography, gas chromatography, and high performance liquid
chromatography (HPLC). In this lecture, the teacher mainly introduced
the principle of HPLC.
HPLC is a technique to separate a mixture of compounds in analytical
chemistry and biochemistry with the purpose of identifying, quantifying
and purifying the individual component. The instruments consists of PUMP
(moves the mobile phase and sample through the column), injector (add
samples), column and detector.
Different liquid chromatography including gel filtration, ion exchange,
affinity and reversed phase chromatography are utilized according to the
protein/peptide properties including size, net surface charge,
hydrophobicity, respectively. Different methods can be combined
according to the purpose, but the most important is keep it simple
because quite a lot of samples are lost during the process.
Thursday, March 29, 2012
Introduction to MS
Mass spectrometry (MS) can identify chemical composition of a sample based on the mass-to-charge ratio of charged particles. The instrument mainly contains three parts including ion source, mass analyzer and detector. The samples are ionized in the ion source using chemical or electron modes. Ions from the ion source were separated according to the m/z ratios in the analyzer part.
Two biological mass spectrometries were introduced during the lecture: Matix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI). Both of them belong to soft ionization methods. The irradiated substance is embedded in crystallized matrix in MALDI. In contrast of MALDI, the ionization in ESI is achieved by spraying a solution into an electrical field. MS has been applied in many fields of protein research including protein identification, molecular weight determination, characterisation of post-translation modifications, relative quantification and also protein complex, etc.
It is important to note that the protein needs to be in solution without salts and detergents and should be purified before the MW measurement. For protein identification, the protein needs to be digested into peptide before analyzing by MS. The identification can base on peptide mass finger print (PMF) and MS/MS data from one or more peptides.
Using Perl script to download sequence from database NCBI
最近发现ncbi上可以用perl scripts 下载序列。虽然是perl,但不需要你来输入命令,你只需输入关键词即可,再就是你的电脑安装了perl。
这就是Ebot!!
Ebot is an interactive tool that generates a Perl script that implements an E-utility pipeline. Ebot will guide you step by step in building the pipeline and then will download the Perl script to your computer.
http://www.ncbi.nlm.nih.gov/Class/PowerTools/eutils/ebot/ebot.cgi
这就是Ebot!!
Ebot is an interactive tool that generates a Perl script that implements an E-utility pipeline. Ebot will guide you step by step in building the pipeline and then will download the Perl script to your computer.
http://www.ncbi.nlm.nih.gov/Class/PowerTools/eutils/ebot/ebot.cgi
Sunday, March 4, 2012
Modk-Prototypes for Simultaneous Clustering of Gene Expression Data with Clinical Chemistry and Pathological Evaluations
Overview
The modk-prototypes algorithm, for clustering biological samples based on simultaneously considering microarray gene expression data and classes of known phenotypic variables such as clinical chemistry evaluations and histopathologic observations involves constructing an objective function with the sum of the squared Euclidean distances for numeric microarray and clinical chemistry data and simple matching for histopathology categorical values in order to measure dissimilarity of samples. Separate weighting terms are used for microarray, clinical chemistry and histopathology measurements to control the influence of each data domain on the clustering of the samples. The dynamic validity index for numeric data was modified with a category utility measure for determining the number of clusters in the data sets. A cluster’s prototype, formed from the mean of the values for numeric features and the mode of the categorical values of all the samples in the group, is representative of the phenotype of the cluster members.
Reference for Citing
Bushel PR, Wolfinger RD and Gibson G. Simultaneous Clustering of Gene Expression Data with Clinical Chemistry and Pathological Evaluations Reveals Phenotypic Prototypes. BMC Bioinformatics 2006.
Data Types and Format
Gene expression data needs to be formatted (short and wide) in a tab delimited text file with array observations as row values and gene, clinical chemistry and histopathology variables as column values. The first row is the column header, the second row is an integer denoting the data type (1 = gene expression, 2 = clinical chemistry measurement, 3 = histopathology observation). The order of the data in the file should be from data type 3 to 2, to 1 and be within individual groups or blocks.
Limitations
Only one categorical feature value per observation is permitted. A feature can exist as only one type of data. The application is optimized for clustering the samples and identifying phenotypic prototypes from the groups of them, not of the genes. The application is not guaranteed to find the optimal solution for the clustering of the samples, just the assignment of the samples to clusters according to the reduction of an objective function close to the global minimum.
Requirements
Modk-Prototypes is a set of Matlab functions and scripts tested in Matlab version 6.5.X.X R13.X for Windows (2000 and XP). You may encounter problems in other operating systems, platforms and/or other Matlab versions. The applications require the Matlab Statistics Toolbox Version 4.0, the Resampling Stats Toolbox Version 1.0 by Daniel T. Kaplan (Department of Mathematics and Computer Science, Macalester College, St. Paul, Minnesota, USA), the adjusted Rand Index function by Tijl De Bie(February 2003), the Matlab loadcell.m function to load mixed type data and the cell2csv.m function to convert cell arrays to comma separate value formatted files, both available at the Matlab Central File Exchange (File ID 1965 and 7601 respectively). Be sure to set the path of the Toolboxes in Matlab before running the application.
Downloads
Download the Matlab files and a stand-alone executable version of the program (http://www.niehs.nih.gov/research/resources/assets/docs/modkprototypesdistributionzip.zip) (101MB) . You will be required to register as a user of the application in order to gauge the distribution and to keep you informed of updates and revisions. A demo script, ReadMe file and sample data are provided in the distribution to help get you started with using the application. Report bugs, corrections and suggestions to Pierre Bushel .
Info:http://www.niehs.nih.gov/research/resources/software/biostatistics/modk/index.cfm
Saturday, March 3, 2012
Clustering analysis of expression microarray data with Subio Platform and Basic Plug-in fwd
Subio Platform is a free, technology-independent omics data browser and software platform for sharing analysis results. Its integrated visualization tools greatly help handling complex omics data and revealing biological insight.
Basic Plug-ins adds analytical functions which are widely used for microarray data analysis. This movie shows how to use the hierarchical clustering analysis to over-viewing too many genes into clusters.
You can see it more clearly.
http://www.screencast.com/t/N2NjZjA2Nzkt
For more information.
http://www.subio.jp/products/basicplugin
Basic Plug-ins adds analytical functions which are widely used for microarray data analysis. This movie shows how to use the hierarchical clustering analysis to over-viewing too many genes into clusters.
You can see it more clearly.
http://www.screencast.com/t/N2NjZjA2Nzkt
For more information.
http://www.subio.jp/products/basicplugin
Friday, March 2, 2012
Microarray Analysis with R
This is a short video introducing R as a language and showing some of its capabilities with microarray data.
protein analysis fwd
Again, a lot of information, but better there are some things you can choose than nothing to choose.
Protein analysis:
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
Molecular Modeling Software fwd
Maybe too many, select the proper one is also challenging!!
modeling software (collected at http://www.mybiosoftware.com).
3DNA 2.0 – Vsualization of Three-Dimensional Nucleic Acid Structures
ActiveICM 1.1.6 – PowerPoint & Web Browsers Plugin to Display 3D Modules
AlloPathFinder 1.1 – Compute Likely Allosteric Pathways in Proteins
AlphaMol 1.0 – Tools for Biomolecular Geometry
AMBER 11 – Assisted Model Building with Energy Refinement
AmberTools 1.5 – Molecular Dynamics Simulation
ANTHEPROT 3D 1.0.162- Molecule Viewer to look at PDB files
APBS 1.3 – Evaluat Electrostatic Properties of Nanoscale Biomolecular System
ArgusLab 4.0.1 – Molecular Modeling, Graphics & Drug Design Program
Ascalaph 1.7.12 – Molecular Modelling Suite
AtVol 1.2 – Atomic Volume Calculation
AUDocker v1 – GUI for AutoDock Vina
Autobondrot 2.0 – Generate Multiple Molecular Conformation
AutoDock 4.2.3 / AutoDockTools 1.5.6 – Suite of Automated Docking Tools
AutoDock Vina 1.1.2 – Molecular Docking and Virtual Screening Program
Autodock/Vina plugin for PyMOL
AutoGrow 2.0.4 – Use AutoDock Vina in Protein Inhibitor Design
Avogadro 1.0.3 – Molecule Editor & Visualizer
AVP 1.3 – Calculate Protein Void Volumes and Packing Quality
AxPyMOL 1.0r1 – PowerPoint Plug-In for Embedding 3D Molecular Images & Animations
B 1.0alpha – Biomolecular Modeling Package
BALLView 2.0-r1 – Molecular Modeling & Visualization
Benchware® 3D Explorer 2.6 – 3D Chemical Visualization
Bioclipse 2.4 – Life Sciences Workbench
Biodesigner 0.75 – Molecular Modeling & Visualization
BioEditor 1.6.1 – Present Macromolecular Structure & Structural Annotation
BioViewer 1.5.7 – Read only version of BioEditor
Biskit 2.3.1 – Python Platform for Structural Bioinformatics
BndLst 1.6 – List Covalent & H-bonded Neighboring Atoms
C2A 1.0 – Coarse to Atomic
CCOMP 3.70 – Compare Ligand/Receptor Complexes
CHARMM 36 – Macromolecular Dynamics and Mechanics
ChemCraft 1.6 – Graphical Program for working with Quantum Chemistry Computation
Chemis3D 2.89b – Java 3D Molecular Viewer Applet
Chemitorium 3.5 – Molecule Editor & 3D Chemical Structure Viewer
Chime 2.6SP8 – Display 2D / 3D Molecules directly in Web Pages
ClashList 1.1 – Build Lists of van der Waals Clashes from PDB file
ClashScore 1.1 – R Script for VTF Percentile Plot
CLICK – Comparison of Biomolecular 3D Structures
Cluster 1.3 – Build Collections of Interacting Items
CN3D 4.3 – 3D Molecular Structure Viewer
CompuCell3D 3.6.0 – 3D Multiscale Multi-cell Simulations
Concoord 2.1 – Protein Structure Generation from Distance Constraint
CONSCRIPT – Generate Electron Density Isosurfaces in Protein Crystallography
Coot 0.6.2 – Macromolecular Model Building Tool
COSMOS 5.0 / COSMOS Viewer 3.0 – Computer Simulation & Visualisation of Molecular Structures
CueMol 2.0.1.161 – Macromolecular Structure Visualization
Dang 1.8 – Read PDB File & Generate Geometric Measurement Table
Dangle 0.63 – Read PDB File & Generate Geometric Measurement Table
DeepView 4.04 – Analyze Several Proteins 3D Structure at the Same Time
Desmond 2.4 – High-speed Molecular Dynamics Simulation
DINO 0.9.4 – Structural Biology Data 3D Visualization
DireX 0.5 – Low-resolution Structure Refinement
DOCK 6.4 – Docking Molecules to each other
DS Visualizer 3.1 & ActiveX Control 3.1 – Molecular Visualization
DTMM 4.2 – molecular modelling program
EDTSurf – Quick and Accurate Construction of Macromolecular Surfaces
EGO VIII – Molecular Dynamics Simulation
eMovie 1.04 – Make Molecular Movies
Facio 15.1.1 – 3D-Graphics program for Molecular Modeling and Visualization
FEATURE 2.0 – Examine Biological Structures
FiltRest3D – Filtering Protein Models by Fuzzy Restraints
FINDSITE 1.0 – Ligand-binding Site Prediction & Functional Annotation
FINDSITE-LHM 1.0 – Homology Modeling Approach to Flexible Ligand Docking
Flex-EM – Fitting and Refinement of Atomic Structures
FlexS 2.0.0 – Predict Ligand Superpositions
Flipkin 2.4 – Script to Make the Kinemages
FMA 0901 – Protein Functional Mode Analysis
FREEHELIX 98 – Analyze DNA bending
FRETsg 1.0 – Structure Building from Multiple FRET Distances
Friend 2.0 – Multiple Structure Visualization & Multiple Sequence Alignment
FTDock 2.0/ RPScore /MultiDock 1.0 – Protein Molecule 3D-Dock Suite
g0penMol 3.0 – Molecules Visualization & Analysis
Gabedit 2.4.0 – Graphical User Interface to Computational Chemistry Packages
GAP 1.2.14 – Geometric Analysis of Proteins
GDIS 0.90 – Visualization Program for Molecular and Periodic Systems
Ghemical 2.99.2 – Molecular Modeling and Editing Package for GNOME
GPGPUFRAGFOLD 0.1 – CUDA Fragment Assembly Based Protein Structure Prediction
Graphite-MicroMégas – Model in 3D Assemblies of Proteins and DNA
GROMACS 4.5.4 – Molecular Simulation
Gromita 1.06 – GUI for GROMACS
g_correlation 1.02 – Generalized Correlation for Biomolecular Dynamics
g_permute 1.12 – Permutation-Reduced Phase Space Density Compaction
HAAD – Quick and Accurate Hydrogen Atom Addition
Hollow 1.1 – Illustration software for Proteins
ICM-Browser 3.7 2b – Molecules & sequence alignments Visualization
iMol 0.40 – Molecular Visualization Application for Mac OS X
iMolview 1.1 – iPhone & iPad App for Browsing Protein, DNA & Drug Molecules in 3D
IMP 1.0 – Integrative Modeling Platform
ISD 1.1 – Bayesian NMR Structure Calculation
ISIM – Simulation of Ions in the Grand Canonical Ensemble
ISIM Interface 1.3.2 – Graphical Interface for running the program
ISIM
Jamberoo 11 – Cross-Platform Molecular Editor & Builder
Jimp 2 0.091 – Visualize and Manipulate Molecules
Jmol 12.0.50 – Java Viewer for Chemical Structures in 3D
JMVS 4 041122 – Java3D Molecular Visualisation System
jSim for Gromacs 0.63b – Graphical User Interface for Gromacs
JyMOL 1.0 – Java-based Molecular Visualization
Kin2Dcont 1.8 & Kin3Dcont 1.12 – Produce Molecule Contour Map
KiNG 2.20 – Three Dimensional Vector Graphics
KinImmerse 0.5 – Translate Kinemage Files into Software for Virtual Environment
LGscore/LGscore2 2.0 – Measure Quality of Protein Model
LifeExplorer 20100108 – 3D Navigation Tool for Cells
LigandScout 3.02 – Pharmacophore 3D Modeling
LoopTK 2.0.1 – Protein Loop Kinematic Toolkit
lrrr 1.4 beta1 – Determines Ligands on the Surface of Proteins
Mage 6.47 – Kinemage File 3D Display
Maptools 1.0 – Deal with Experimental (X-ray, EM) 3D Maps
MapVol 1.1 – Awk Script to Assign Volume by Atom
MaSK 1.3.0 – Molecular Modeling and Simulation Kit
MD Morphing 1.0 – Perform Molecular Dynamics Morphing Simulations
MDynaMix 5.2 – Molecular Dynamics Program
MetaTASSER – Protein Structure Prediction tool
MGLTools 1.5.6RC2 – Visualization & Analysis of Molecular Structures
MINT 3.2 – User Interface to Modeller
MMB 2.4 – Model the Structure and Dynamics of Macromolecules
mmPDBViewer 2009.3.20.4 – Protein Data Bank Viewer
MMPRO 0.7 – Molecule Visualization & Analysis Program
MMTK 2.7.4 – The Molecular Modelling Toolkit
MMTSB toolset – Multiscale Modeling Tools for Structural Biology
MMV 2.2.0 – Visualization of Molecules
ModeHunter 1.1 – Normal Mode Analysis of Coarse Grained Elastic Networks
MODELLER 9.10 – Comparative Protein Structure Modeling
Models@Home 4.5 – Distributed Computing Software for Protein Modeling
ModeRNA 1.6 – Comparative RNA 3D Modeling
ModPipe 2.2.0 – Calculate Protein Structure Model
ModRefiner 20111024 – High-resolution Protein Structure Refinement
ModView 0.903 – Visualization of Multiple Protein Sequences & Structures
MOIL 12.0.3671 – Molecular Modeling Software
Móilín 2011 – Molecular Modelling Software
Mol2Mol 5.6.3 – Molecule File Manipulation & Conversion
MOLA – System for Virtual Screening using AutoDock4/Vina on Computer Clusters
MolIDE 1.7 – Protein 3D Homology Modeling
MolPOV 2.0.8 – PDB to POV File Converter & Visualizer
MolScript 2.1.2 – Display Molecular 3D Structures
MolTalk 3.0.1 – Computational Environment for Structural Bioinformatics
MoluCAD 1.034 – Molecular Modeling & Visualization Tool
MoSART pr – NMR-based Biomolecular Structure Computation
MSMExplorer 0.02 – Visualization Application for Markov State Models for Folding
MVP/MVP-Fit 2.0 – Macromolecular Visualization and Processing
NAContacts 2.5 – Write Contact Information between Nucleic Acid Bases
NAST 1.0 – Nucleic Acid Simulation Tool
NMFF – Normal Mode Flexible Fitting
NOC 3.01 – Molecular Explorer for Protein Structure Visualization
OB Score 1.0 – Structural Genomics Target Ranking
OpenAstexViewer 3.0 – Software for Molecular Visualisation
OpenMM 3.1.1 – Library for Molecular Modeling Simulation
OpenMM Zephyr 2.0.3 – Molecular Simulation Application
OpenStructure 1.1.0 – Computational Structural Biology Framework
ORTEP-III 1.03 – Crystal Structure Illustration
Oscail 2011 – Crystallography & Molecular Modelling
OVOP 1.0 – View Generation for Protein Structures
PaDEL-ADV 1.6 – Facilitate Virtual Screening with AutoDock Vina
PDB Editor 090203 – PDB (Protein Data Bank) File Editor
PDBCNS 2.0 – Interconvert Atom Names between PDB & CNS formats
PDBlib 2.2 – C++ Macromolecular Class Library
PDBpy – Python Parser for PDB files
PeppeR 0.8.160 – Graphical 3D-EM DAS Client
PHENIX 1.7 – Python-based Hierarchical ENvironment for Integrated Xtallography
PovChem 2.1.1 – Chemical Visualization & Illustration & POV File Converter
Prekin 6.51 – Prepares Kinemages Files from PDB-format Files
PREPI 0.9 – Molecular 3D Representation
Probe 2.12 – Evaluate Atomic Packing & Contact Analysis
ProbeWithO 0.9.0 – Use Small Probe Contact Dots Within O
ProFit 3.1 – Protein Least Squares Fitting
ProSa 2003 – Protein Structure Research Tool
PROTEAND 1.0 – Display Macromolecular Structural Uncertainty
Protein Explorer 2.80 – Visualize 3D Structures of Macromolecules
ProteinGlimpse 1.6 – Visualize Macromolecules Retrieved from PDB
ProteinScope 1.0.5 – 3D Protein Structure Viewer
ProteinShader beta 0.9.4 – Illustrative Rendering of Macromolecules
ProtoMol 3.3 – Molecular Dynamics (MD) Simulation
PULCHRA 3.06 – All-atom Reconstruction & Refinement of Reduced Protein Models
pymacs 0.4 – Python Module for Dealing with Structure files from GROMACS
PyMOL 1.4.1 – Molecular Visualization System
PyOpenMM 3.0 – Python API of OpenMM Library
PyRx 0.8 – Virtual Screening software for Computer-Aided Drug Design
QTree 2.3 – Graphics Rendering using Quad-tree Algorithm
QuickPDB 20021101 – Java Applet for quickly viewing PROTEIN PDB Structure
QuteMol 0.41 – Molecular Visualization System
R.E.D. III.4 – Calculate RESP Charges
Ramachandran Plot Explorer 1.0 – Interactive Cross-platform Protein Viewer
Rasmol 2.7.5.2 – Molecular Graphics Visualisation
Raster3D 3.0-2 – Generate High Quality Raster Images of Proteins or other Molecules
RasTop 2.2 – Molecular Visualization Software Adapted for Rasmol
RDCvis 1.02 – Residual Dipolar Coupling Visualizer
Reduce 3.14 – Add Hydrogens to PDB Molecular Structure File
Remediator 1.60 – Convert PDB Files between PDBv2.3 & PDBv3.2 Formats
REMO 1.0 – Construct Full-atom Protein Models from C-alpha Traces
Ribbons 3.32 – Molecular Graphics Software
RIP 1.0 – Accelerated Molecular Dynamics
RNABC 1.11 – RNA Backbone Correction
Rosetta@home – Grid Software for Protein Folding
rTools 0.7.2 – PyMOL plugins
ScoreDotsAtAtom 1.0 – Bookkeep All-atom Contact Dot
Sculptor 2.0.2 – Docking & Visualization for Atomic Structures
SEQMOL 3.4.6 – Sequence Alignment & PDB Structure Analysis Utility
SHIFTS 4.3 – Predict Nitrogen, Carbon & Proton Chemical Shifts in Proteins
SimTK Core 2.1 – Simbios Biosimulation ToolKit
Situs 2.6 – Integration of Multi-Resolution Structures
Solvate 1.0 – Construct Atomic Solvent Environment Model for Given Atomic Macromolecule Model
StrukEd – Editor for Molecules & 3D Viewer
Suitename 0.3 – RNA Conformer
Superficial 1.2 – Identification of Potential Epitopes or Binding Sites
SuperMimic – Fit Peptide Mimetics into Protein Structures
TASSER-Lite 1.0 – Protein Structure Modeling tool
tCONCOORD 1.0 – Predict Protein Conformational Flexibility
Tessellator 1.0 – Software for Tessellation of 3D Volume in Biological Molecule
Theseus 1.6.1 – Superimpose Macromolecular Structures
THREADER 3.51 – Protein Fold Recognition by Threading
TimeScapes 1.2.2 – Molecular Dynamics Analysis tool
Tinker 5.1.09 – Software Tools for Molecular Design
Torsions – Calculates Backbone Torsion Angles from a PDB file
UCSF Chimera 1.5.3 – Molecular Modeling System
VcPpt – Protein Ligend Docking & in silico High-throughput Screening
VEGA ZZ 2.4.0 – Molecular Modeling Toolkit
VESTA 3.0 – 3D Visualization System for Electronic & Structural Analysis
Viewmol 2.4.1 – Molecule Viewer
ViewMol3D 5.00.alpha.3 – 3D OpenGL Viewer for Molecular Structures
VisProt3DS 3.03 – Stereoscopic Visual Analyzer of Biological Macromolecules
VMD 1.9 – Molecular Graphics Viewer
Voronoia 1.0 – Analyse Packing of Protein Structures
WebMol – JAVA PDB Viewer
WPDB 2.2 – The Protein Data Bank Through Windows
XCrySDen 1.5.24 – Crystalline & Molecular Structure Visualisation
XmMol 3.1 – Macromolecular Visualization and Modeling tool
XtalView 4.0 – Molecular Graphics Program
YAKUSA – Scan Structural database with Query Protein Structure
YASARA 11.9.18 – Molecular Graphics, Modeling & Simulation program
YUP 1.080827 / Yammp 2 – Molecular Simulation
Zodiac 0.6.5 – Molecular Modelling suite for Drug Design
HyperBalls Viewer – Molecular structures and trajectories visualization using GPU rendering
modeling software (collected at http://www.mybiosoftware.com).
3DNA 2.0 – Vsualization of Three-Dimensional Nucleic Acid Structures
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