Holy Cross College
Bioinfomatics Infrastructure Facility (BIF)

Sponsored by DBT.BTIS, Ministry of Science & Technology, Govt. of INDIA

Resources

Department of Biotechnology and Bioinformatics

Sequence Analysis

BioEdit 
BioEdit is a full integrated sequence/alignment editor. Performs translations, phylogenetic analysis, clustalw alignments, ABI trace analysis, RNA comparative analysis and BLAST searches.
URL: http://www.mbio.ncsu.edu/BioEdit/bioedit.html 

Blast
BLAST 2.0, (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases.
URLhttp://www.ncbi.nlm.nih.gov/toolbox/ncbi_tools/ 

Boxshade
BOXSHADE is a program for creating good looking printouts from multiple-aligned protein or DNA sequences. The program does no alignment by itself, it has to take as input a file preprocessed by a multiple alignment program or a multiple file editor.
URLhttp://www.isrec.isb-sib.ch/pub/ 

Circle 
Infer RNA secondary structure using the comparative method.
URLhttp://taxonomy.zoology.gla.ac.uk/rod/circles/ 

ClustalW 
Clustal-W is a multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results.
URLhttp://www.ebi.ac.uk/pub/software/unix/clustalw/ 

ClustalX 
ClustalX is a new windows interface for the ClustalW. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results.
URLhttp://www.ebi.ac.uk/pub/software/dos/clustalx/

Dambe Windows
It is a general-purpose package for DNA and protein sequence phylogenies, and also gene frequencies.
URLhttp://aix1.uottawa.ca/~xxia/software/software.htm

DCSE
DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment.
URL: http://rrna.uia.ac.be/dcse/ 

DNA 
DNATools is a comprehensive program package for routine handling and analysis of nucleotide and protein sequences. The program includes functions for batch renaming, editing and annotating sequences, restriction mapping, translation, automated blast search and information retrieval, codon analysis, primer design and ordering and a lot more...
URLhttp://www.crc.dk/dnatools/

DNA Club 
PC program for Integrated analysis on DNA sequences.
URLhttp://softwareseek.progenote.net/downloads/ 

Emboss
EMBOSS, The European Molecular Biology Open Source Software Suite, is a package of high-quality FREE Open Source software for sequence analysis.
URLhttp://emboss.sourceforge.net/ 

FastA 
The FastA program has been developed by Pearson & Lipman (1988) and is useful to find all protein sequences of a database such as Swiss-Prot, that are homologous to a given sequence.
URLhttp://www.ebi.ac.uk/fasta33/ 

GeneDoc 
GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.
URLhttp://www.psc.edu/biomed/genedoc/ 

Hmmer
A profile hidden Markov model that can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
URLhttp://hmmer.wustl.edu/ 

HyPhy 
It intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. HYPHY was designed with maximum flexibility in mind and to that end it incorporates a simple high level programming language which enables the user to tailor the analyses precisely to his or her needs. These include relative rate and ratio tests, several methods of ML based phylogeny reconstruction, bootstrapping, model selection, positive selection, molecular clock tests and many more...
URLhttp://www.hyphy.org/ 

JalView 
Graphical multiple alignment editor. Requires Java Virtual Machine.
URLhttp://www.jalview.org/ 

Jemboss

Jemboss is developed by the EMBOSS team. The software is free and part of the EMBOSS distribution.
URLhttp://emboss.sourceforge.net/Jemboss/ 

Mega3 
MEGA is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
URLhttp://www.megasoftware.net/

MFold 
Mfold is an RNA and DNA folding package.
URLhttp://www.bioinfo.rpi.edu/~zukerm/export/mfold-3.html

NCBI ToolKit 
The NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.
URL: http://www.ncbi.nih.gov/toolbox/ncbi_tools/

PeptideMass 
The Program cleaves a protein sequence from the UniProt Knowledgebase (Swiss-Prot and TrEMBL) or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest 
URLhttp://www.expasy.ch/tools/peptide-mass.html

RNA DRAW 
It is an integrated program for RNA secondary structure calculation and analysis.
URLhttp://www.rnadraw.com/ 

Readseq
Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences.
URLhttp://iubio.bio.indiana.edu/soft/molbio/readseq/ 

Seaview 
SeaView is a graphical multiple sequence alignment editor. It is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment.
URLhttp://pbil.univ-lyon1.fr/software/seaview.html 

Sequence Manipulation Suite 
The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.
URLhttp://bioinformatics.org/sms2/ 

Vienna RNA Package 

RNA Secondary Structure Prediction and Comparison.
URLhttp://www.tbi.univie.ac.at/~ivo/RNA/ 

WinGene
 
A tool for the analysis of nucleotide sequences.
URL: http://www.ipw.agrl.ethz.ch/~lhennig/wingene.html 

X3DNA

3DNA is a versatile package for analyzing and rebuilding three-dimensional nucleic acid structures, based on a standard reference frame.
URLhttp://rutchem.rutgers.edu/~xiangjun/3DNA/

 

Phylogenetic Analysis

CoPE 
A collaborative pedigree drawing environment 
URLhttp://www.infobiogen.fr/services/CoPE/

FreeTree 
Freeware program for construction and bootstrap (and jackknife) analysis of phylogenetic trees from binary data (RAPD, RFLP, AFLP etc.)
URLhttp://www.natur.cuni.cz/~flegr/programs/freetree.htm 

GeneTree 
GeneTree is an experimental program for comparing gene and species trees.
URLhttp://www.stats.ox.ac.uk/~griff/software.html 

PHYLIP 
PHYLIP is a free package of programs for inferring phylogenies.
URL: http://evolution.genetics.washington.edu/phylip.html 

PhyloDraw 
PhyloDraw is a drawing tool for creating phylogenetic trees. It supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams.
URL: http://pearl.cs.pusan.ac.kr/phylodraw/ 

TreeView 
TreeView X is an open source program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs).
URLhttp://darwin.zoology.gla.ac.uk/~rpage/treeviewx/index.htm

 

Genomics

Artemis 
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. 
URL: http://www.sanger.ac.uk/Software/Artemis/ 

Chromas 
It will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create.
URLhttp://www.technelysium.com.au/chromas.html 

GenAl 
GenAl is a program for genomic alignment, i.e. alignment of DNA sequences with coding regions. It is an implementation of the heuristic algorithm described in Hein, J. & J. Stoevlbaek (1994): Genomic Alignment. J. Mol. Evol.
URLhttp://www.ebi.ac.uk/pub/software/unix/

Genome Workstation 
Genome Related Links at Roslin Institute, UK 
URL: http://www.ri.bbsrc.ac.uk/genome_workstation/workstation.html

Genomes OnLine Database (GOLD 1.0) : - 
A monitor of complete and ongoing genome projects world-wide. 
URLhttp://wit.integratedgenomics.com/GOLD/

Glimmer 
A system for finding genes in microbial DNA, especially the genomes of bacteria and archaea.Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
URLhttp://www.tigr.org/software/glimmer/ 

Glimmer HMM 
A fast and accurate gene finder based on a GHMM architecture,
developed specifically for eukaryotes. It incorporates splice site models adapted from the GeneSplicer program and uses interpolated Markov models for evaluating the coding regions.
URLhttp://www.tigr.org/software/GlimmerHMM/ 

Glimmer M 
A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programming algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. The decision about what gene model is best is a combination of the strength of the splice sites and the score of the exons generated by an interpolated Markov model (IMM).
URLhttp://www.tigr.org/software/glimmerm/

MUMmer 
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
URLhttp://www.tigr.org/software/mummer/ 

PDRAW 
pDRAW32 is being developed as a free time hobby project. It is far from finished, but as it has reached a point where it could be helpful for many labs, it is now available to the scientific community.
URL: http://www.acaclone.com/ 

PrimerDesign 
Primer Design is a DOS-program to choose primer for PCR or oligonucleotide probes. It is tailored to check known sequences for repeats and unique sequences and subsequently to create prober primers according to this data. A lot of constrains are available to meet your conditions. It can handle up to 32000 base pairs.
URLhttp://www.bioinf-club.com/software/ 

Sequin
Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, segmented sets of DNA, or phylogenetic and population studies.
URLhttp://www.ncbi.nlm.nih.gov/Sequin/ 

Staden

The Staden Package consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DNA/protein sequence analysis (spin).
URLhttp://staden.sourceforge.net/ 

 

Proteomics

ADVICE Web
Automated Detection and Validation of Interaction by Co-Evolution (ADVICE) takes a list of protein sequences or sequence pairs as input and uses orthologous sequences to assess the similarity in the evolutionary history of the proteins. It is suggested that co-evolution of proteins is useful for predicting and validating protein-protein interactions.
URLhttp://advice.i2r.a-star.edu.sg/ 

ANTHEPROT 
ANTHEPROT (ANalyse THE PROTeins) is to integrate into a single package most of the methods designed for protein sequence analysis.
URLhttp://antheprot-pbil.ibcp.fr/ 

CNplot 
CNplot is a network visualization tool that can be used for large-scale networks, as long as they are pre-clustered.
URLhttp://csb.stanford.edu/~nbatada/VCN.html 

Graphviz 

Graph layout software for protein network.
URLhttp://www.graphviz.org/ 

InterViewer 
InterWeaver is a tool employing two approaches to detect potential protein interactions by searching for and interpreting evidence available from on-line databases. The first approach finds homologues for a sequence and searches for interacting partners in protein interaction and literature databases, and the second finds sequence domains, and then searches for domain fusion events and possible domain interactions.
URLhttp://wilab.inha.ac.kr/protein/ 

Osprey 
Application for graphically representing physical and genetic biological interactions; is coupled with the General Repository of Interaction Datasets (The GRID); available for Unix and .
URLhttp://biodata.mshri.on.ca/osprey/servlet/Index

Pajek 
Program for Larger Network Analysis.
URLhttp://vlado.fmf.uni-lj.si/pub/networks/pajek/default.htm 

PIN 
To visualize the protein's interaction and function annotations. The software allows the user to search for information on putative protein interactions and function classes. 
URL: http://www.bioinfo.org.cn/PIN/ 

Teverna 
Taverna is a tool for creating and running bioinformatics workflows.
URLhttp://taverna.sourceforge.net/ 

WinPep 

A versatile tool for the analysis of amino acid sequences.
URLhttp://www.ipw.agrl.ethz.ch/~lhennig/winpep.html 

 

Molecular Visualization

MOLMOL 
MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.
URLhttp://hugin.ethz.ch/wuthrich/software/molmol/ 

Molscript 
A program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
URLhttp://www.avatar.se/molscript/ 

Rasmol 
Rasmol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules.
URLhttp://www.umass.edu/microbio/rasmol/index2.htm 

Raster 3D 
Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware.
URL: http://www.bmsc.washington.edu/raster3d/raster3d.html 

SPDBViewer 
Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
URLhttp://au.expasy.org/spdbv/ 

 

Systems Biology

Cellware 
Cellware has been designed to conduct modeling and simulation of gene regulatory and metabolic pathways and also offer an integrated environment for diverse mathematical representations, parameter estimation and optimization. In addition, a user-friendly graphical display and capability to run large and complex models would be provided by default. A very special feature of Cellware is that it would be the first grid based modeling and simulation tool in the field of Systems Biology.
URLhttp://www.bii.a-star.edu.sg/research/sbg/cellware/ 

CytoScape 
Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions.
URLhttp://www.cytoscape.org/

E-Cell 3 
E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.
URLhttp://www.e-cell.org/ 

Gepasi 
Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and linear stability analysis.
URL: http://www.gepasi.org/ 

 

Molecular Modeling

[FTDock, RPScore and MultiDock]
FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information.
URL: http://www.bmm.icnet.uk/docking/ 

ArgusLab 
It is an incredible molecular modeling, graphics, and drug design program.
URL: http://www.planaria-software.com/ 

Biodesigner 
It is a molecular modeling and visualization program for personal computers which is capable of creating homologous models of proteins, evaluate, and refine the models.
URLhttp://www.pirx.com/biodesigner/index.shtml 

Chem2Pac 
Chem2Pac is intended to be a kind of computational chemistry integrator, which has a multiple document interface, a molecular rendering utility, and allows the manipulation of various files.
URLhttp://www.ifi.unicamp.br/gsonm/chem2pac/ 

Cn3D 
Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.
URLhttp://ncbi.nih.gov/Structure/CN3D/cn3d.shtml 

Dang 
Dang reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each residue or base. In its most basic form, it writes out dihedral angles (phi, psi, chi) hence the name. The output is formatted for easy parsing by awk, grep, sort and other UNIX utilities.
URLhttp://kinemage.biochem.duke.edu/software/dang.php 

DomainFinder 
It is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are computational efficiency: even large proteins can be analyzed using a desktop computer in a few minutes ease of use: a state-of-the-art graphical user interface export of results for visualization and further analysis (VRML, PDB, and MMTK object format).
URLhttp://dirac.cnrs-orleans.fr/DomainFinder/ 

Easy Winbabel 
It's a program for chemists and physicists dealing with molecular modeling. It uses the well known BABEL program as basis and provides a windows interface. The zip file includes BABEL ver 1.6.
URL: http://users.uoi.gr/nkourkou/babel.html 

EDPDB 
EdPDB is a program to manipulate and extract information from Brookhaven Protein Databank (PDB) format coordinate file(s) of three-dimensional protein structures.
URLhttp://omega.omrf.ouhsc.edu/zhangc/edpdb/edpdb.html 

Garlic 
It is a free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, , free software download, open source software.
URLhttp://garlic.mefos.hr/garlic-1.0/ 

Ghemical 
Ghemical is a computational chemistry software package released under the GNU GPL. Geometry optimization, molecular dynamics and some visualization tools are currently available. If quantum-mechanical calculations are needed, Ghemical can be directly linked into the quantum chemistry program MPQC (which is also distributed under GNU GPL). Therefore Ghemical can serve as a graphical front-end for the MPQC program, currently providing various 3D-plots for electron densities, molecular orbitals and molecular orbital densities.
URLhttp://www.uku.fi/~thassine/ghemical/ 

gOpenMol 
gOpenMol graphics interface to the OpenMol and can be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbital's, electron densities and electrostatic potentials.
URL: http://www.csc.fi/gopenmol/ 

GRAMM 
GRAMM is a program for protein docking. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules (no information about the binding sites is needed). The program performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules. The molecular pairs may be: two proteins, a protein and a smaller compound, two transmembrane helices, etc. GRAMM may be used for high-resolution molecules, for inaccurate structures (where only the gross structural features are known), in cases of large conformational changes, etc.
URLhttp://www.chem.ac.ru/Chemistry/Soft/GRAMM.en.html 

GROMACS 

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
URLhttp://www.gromacs.org/ 

HEX 
Hex is an interactive protein docking and molecular superposition program. Currently, Hex understands protein and DNA structures in PDB format.
URLhttp://www.csd.abdn.ac.uk/hex/

KineMage 
A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond immediately: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated.
URLhttp://kinemage.biochem.duke.edu/kinemage/magepage.php 

LOOPP 
LOOPP is a fold recognition program based on the collection of numerous signals, merging them into a single score, and generating atomic coordinates based on an alignment into a homologue template structure.
URLhttp://cbsu.tc.cornell.edu/software/loopp/index.htm 

MOIL 
MOIL is a molecular modeling software, which is in the public domain, and is written in the group of Ron Elber. Available features, such as energy calculations, minimization and calculations of classical trajectories. Graphic User Interface for a wide range of moil applications on a Windows desk. This interface enables direct calculation on a desktop, on a Windows cluster, and on properly configured web servers.
URLhttp://cbsu.tc.cornell.edu/software/moil/moil.html 

NAMD 
NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code.
URL: http://www.ks.uiuc.edu/Research/namd/ 

NOC 
It is a free program for protein structure model-building, visualization, validation and analysis.
URL: http://noc.ibp.ac.cn/ 

OpenBable 
Open Babel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.
URL: http://openbabel.sourceforge.net/ 

Reduce 
Reduce is a program for adding hydrogens to a Protein Data Bank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided. A slightly modified version of the connectivity table published by the PDB is included (reduce_het_dict.txt).
URLhttp://kinemage.biochem.duke.edu/software/reduce.php 

TraX 
TraX (Trajectory eXplorer) is a simple Biodesigner-like program working under and Windows. The program allows reading a protein folding simulation trajectory (TRA file) and saving a single frame as a PDB file.
URLhttp://www.pirx.com/biodesigner/download.html 

VEGA 

VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modeling suite.
URLhttp://users.unimi.it/~ddl/ 

 

Structure Alignment

ALIGN:- 
Optimal Global Alignment of Two Sequences with No Short-cuts
URLhttp://www.biochem.ucl.ac.uk/bsm/dbbrowser/ALIGN/ALIGN.html 

PROCHECK :- 
Evaluates the quality of a protein structure by Roman Laskowski, University College, London 
URLhttp://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html

PROVE :- 

Analysis of Protein Atomic Volumes at UCMB, Belgium 
URLhttp://www.ucmb.ulb.ac.be/UCMB/PROVE/

WHAT IF :- 
A versatile structure analysis program for mutant prediction, structure verification, molecular graphics and more by Gert Vriend, EMBL, Germany 
URLhttp://swift.cmbi.ru.nl/servers/html/

 

Tutorials

Nucleic acid sequence analysis: 
http://www.bmb.psu.edu/597a/students/byn1/mdm.htm 
http://www.psu.edu/general/software/categories/sequence-analysis.html 
http://ndbserver.rutgers.edu/NDB/archives/NAnitro/index.html 
http://www.library.csi.cuny.edu/~davis/Biochem_3521/pronuclinfoweb.html#NUCLEICACID

Protein sequence analysis 
http://www.nbif.org/education/tutorial.php#Tutorial1 
http://ndbserver.rutgers.edu/structure-finder/tutorials/index.html 
http://www.mcc.ac.uk/hpc/mantec/training/bioinformatics/tools/InetToolsBio_26.html 
http://www.library.csi.cuny.edu/~davis/Biochem_3521/pronuclinfoweb.html#PROTEIN

Metabolic pathways 
http://www-unix.mcs.anl.gov/compbio/PUMA/Production/puma.html 
Function prediction 
http://www.genome.ad.jp/manuscripts/GIW95/Oral/GIW95O05.html 
http://www.cs.uga.edu/~eileen/bioinform/tsld023.htm

Structure prediction & analysis 
http://www.bmm.icnet.uk/people/rob/CCP11BBS/flowchart2.html 
http://ismb00.sdsc.edu/tutorials/samudrala.html 
http://www.biochem.ucl.ac.uk/~shepherd/ss-intro.html#why_is 
http://www.embl-heidelberg.de/predictprotein/predictprotein.html 
http://www.bmerc-www.bu.edu/psa/

 

DaiCee

Database for Identification of Cancer Effects

The database is the collection of cancer drugs with their physiochemical and structural properties, their cancer targets and side-effects



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