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Recursos Externos

Genetic Code, IUBMB Degeneracies, Amino Acids, Amino acid chemical properties...


Main Online Collections of Resources - Bioinformatics META-SERVERS

National Institutes of Health Molecular Biology Resources

Computational Molecular Biology at NIH

European Molecular Biology Laboratory

EMBL Toolbox

InterProScan

Swiss Institute of Bioinformatics

ExPASy Proteomics Server | Expasy Links

Institut Pasteur

Bioweb

Weizmann Institute Bioinformatics and Biological Computing

Toolbox

Center for Biological Sequence Analysis .dk

Services

OpenWetWare

Sharing Information, know-how and wisdom among researchers


General Databases

DNA

GenBank NCBI

Nucleic Acid Database

EMBL Nucleotide Sequence Database

DNA Databank of Japan

Protein

Protein Data Bank RCSB PDB

Protein Data Bank EMBL PDBe

Protein Data Bank Japan PDBj

PDBsum Enzyme Structures Database (Enzyme Classification E.C.)

DALI: Structural Neighbors Protein Database - 3D Structural Comparison

PROSITE: Database of protein domains, families and functional sites

Relibase - Searching protein-ligand databases

SPIN - Protein Protein Interfaces

Protein Mutant Database

NCBI Structure Group Resources

Brenda: The Comprehensive Enzyme Information System

MEROPS - The peptidase database

Proteopedia - The free, collaborative 3D-encyclopedia of proteins & other molecules -

Metabolic Pathway Databases

SMPDB - Small Molecule Pathway Database

KEGG - Kyoto Encyclopedia of Genes and Genomes

MetaCyc

HumanCyc

BioCyc

Reactome

Chemical Compound or Compound Specific Databases

PubChem

Organic Chemistry.org

ChEBI

ChemSpider

KEGG Glycan

Toxin Target Database

Drugs

Drugbank

Miscellaneous

Drugbank Database Collection

REBASE: The restriction enzyme database

Double Digest Finder

Molmovdb: Database of Macromolecular Movements

University of Minnesota Biocatalysis and Biodegradation Database

Codon Usage Database

EcoCyC E.coli Database

Organic Chemistry Portal - The Organic Chemistry Portal offers an overview of recent topics, interesting reactions, and information on important chemicals for organic chemists.

The Merck Index - Organic Name Reactions

DrugBank - The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information -

ChemID Plus - Dictionary of over 370,000 chemicals (names, synonyms, and structures). Includes links to NLM and other databases and resources -

ToxNet - Databases on toxicology, hazardous chemicals, environmental health, and toxic releases -

Databases at Rostlab

Genesilico.pl - interesting selection of servers and resources-

Web servers at Institute of Microbial Technology, Chandigarth, India.

KEGG PATHWAY Database - Wiring diagrams of molecular interactions, reactions, and relations

Panther Database - The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.

Honig Lab Software Tools

Departamento de Genética - Cinvestav Links


Sequence Search

BLAST: Basic Local Alignment Search Tool

FASTA - sequence similarity searching against protein databases using the FASTA programs -

Instaseq - Georgetown

CDART: Conserved Domain Architecture Search Tool

Mega Software - an integrated tool for conducting automatic and manual sequence alignment,
inferring phylogenetic trees, mining web-based databases, estimating rates
of molecular evolution, and testing evolutionary hypotheses. -

Biology Workbench - search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems. -

UGENE - free cross-platform genome analysis suite -

Pairwise Sequence Alignment

EMBOSS

Multiple Sequence Alignment

ClustalW

Mamooth

Strap

Jalview


Molecular Biology Suites

VectorNTI

Bioedit

EMBOSS - European Molecular Biology Open Software Suite

Gene Designer 2.0 (free)

Molecular Visualization Software

PyMOL

RasMol

Swiss-PDB Viewer DeepView

Chimera

Cn3D

Accelrys Discovery Studio Visualizer

VMD - Visual Molecular Dynamics

Yasara

Molscript "Molecular 3D Structure Program"

Raster3D

Chemscape Chime

Swiss-Pdb Viewer

MOLOC

Vega ZZ

"The Molecular Level" Tools for Structural Biology Education and Training. Prof. Dr. Gale Rhodes

Principles of Protein Structure


3D Graphics Creation

Pov-ray The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics.


Protein Structure Prediction Servers

Definition of Protein Structure Prediction - Wikipedia

Classification of Protein Structure Prediction Software (ab initio, homology m., threading)

Protein Structure Prediction Center - CASP

Best Servers and Services According to the Protein Structure Prediction Center

Additional Services of the Protein Structure Prediction Center

Phyre (threading based)

Zhang´s Lab - I-Tasser

David Baker´s Lab - Robetta

Rosetta (ab initio based)

David Baker´s Lab - Rosetta@home

ProtInfo

CPHmodels

SwissModel

3D-Jigsaw

Loop

Homodeller

Prospect

Pcons

Protein Structure Predition Services at Rostlab predictprotein.org

Protein Structure Prediction at Genesilico

Secondary Structure Prediction

JPred

GOR

SOPMA

DSSP

Homology Modelling Software

MODELLER

Check Model Quality

PROCHECK

ProSA

ProQ

SAVES

Protein Structure Comparison

DALI

PDBeFold

CE

FATCAT

Classification of Protein Structures

COPS

Analyze Evidence of Flexibility in a Crystal Structure

TLSMD

Protein Superposition Servers

Superpose 1.0

PDBeFold

TM-align Zhang Lab

DALI

Matras

Protein Meta Functional Determination

ProtInfo

Function Prediction Servers at Rostlab

Protein Surface Accessibility and Secondary Structure

NetSurfP

Protein Hidrophobicity Plots

Plots

Protein Antigenicity Plot

JaMBW

Protease Cleavage Sites

Peptide Cutter

Calculate Protein Physical and Chemical Parameters

ProtParam

Cysteine Disulphide Bond Prediction from Protein Sequence

CysState

Will this protein fold?

FoldIndex

iFold

Protein Folding Server

Peptide Solubility Servers

Proso

Peptide Property Calculator

Recombinant Protein Solubility Prediction

Protein Stability an Design

FoldX - FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.

ProfBval

Classification and Secondary Structure Prediction of Transmembrane Proteins

SOSUI

Prediction of transmembrane helices in proteins

TMHMM

Web-accessible database linking PDB chains to EC numbers

PDBSProtEC

Tools to evaluate interactions between amino acids

Amino acid Structure and Classification

The Amino Acid Repository - Jena Library of Biological Macromolecules

AAindex

Atlas of Amino acid side-chain interactions: sidechain-sidechain and sidechain-DNA

The single residue contact server

Disulphide bond database

Evaluation of mutation effects

WHATIF


Active Site Finders

Catalytic Site Atlas

Active Site Prediction Server

Qsite finder - ligand binding site

CASTp - Computed Atlas of Surface Topology of Proteins


Automatic Identification of Active Site and Hot Spots for Protein Engineering

Hotspot Wizard

About Hotspot Wizard (Read it!)


Library Creation Tools for Directed Evolution

CASTER & B-FITTER

Statistics of Randomized Library Construction


Automatic 2D representation of Protein-Ligand and Protein DNA interactions

LigPlot

NucPlot

Subcellular Localization Prediction Tool

PSORTb

Prediction of Signal Peptides

PrediSI

Signal IP


Biomolecular Docking and P-P or P-L Interactions Servers

Zdock

Protein Drug Contact

String

KFC Server

Hex

PatchDock

HotSprint

RosettaDock

Escher NG

Chemera and Bigger

SuMo

LPC/CSU

DOT 2.0

3D-Garden

HADDOCK

FireDock

Protorp

Curie Servers

SHARP2

meta-PPISP

APID

TOPS

PEARLS

ClusPro

Protein Ligand docking and in silico high throughput screening for Windows

Binding Moad Database

Similarity ensemble approach (SEA)

Protein Interaction Servers

The Binding Database

Procognate


Docking Programs

Autodock

Dock

Dock Blaster

Docking.org

ArgusLab

FRED

Molecular Docking Web

Molecular Dynamics

GROMACS

NAMD

Hyperchem (€)

Schrödinger Maestro Molecular Modeling Platform (€)

Accelrys Dicovery Studio (€)

Tripos Benchware Discovery 360 (€)

Chemical Drawing

ACDLabs

ChemBioOffice

Isis

Transform 2D in 3D online

Open Babel

Molsoft


PCR based gene synthesis

DNAworks

TmPrime

Gene2Oligo

GeneDesign

Optimized Gene Design

DNA 2.0

Visual Gene Developer

Optimizer

Gene synthesis & more - companies -

Geneart

Sloning

Biomatik

GenScript

Invitrogen


Buffer Calculator

University of Liverpool

In-silico simulation of Molecular Biology Experiments

University of the Basque Country. Vitoria-Gasteiz, Spain.

Electronic Communication Forums

Biosci/Bionet

Predict Protein | Rostlab Twitter

Online Conferences

Ted.com

Scientific Videos

Youtube

DNAtube

SciVee


Public Microbial Libraries       

Colección Española de Cultivos Tipo [CECT] | Servicios

American Type Culture Collection [ATCC]

German Culture Collection [DSMZ]

National Collection of Yeast Cultures [NCYC] U.K.

Centraalbureau voor Schimmelcultures [CBS] ND

International Mycological Intitute [IMI] U.K.

Belgium Microbial Collection


Chemical Suppliers - Substructure search engines

Directory at organic-chemistry.org
Sigma-Aldrich ABCR Acros Organics
ABCR Alfa-Aesar Strem

Crystallography

Crystallography made crystal clear - Gale Rhodes

Gale Rhodes Home Page

Hampton Research

EMBL-Hamburg

Ruppweb - Crystallography 101

The Protein Crystallization Home Page of Terese Bergfors

X-Tal Protocols

Other Link Collections of Interest

OpenWetWare - Research Groups Wiki Network

VADLO - Search engine for biology and medical powerpoints, methods, techniques, reagents, bioinformatics resources.

Proteopedia

Protein Lounge

UCLA Institute of Genomics and Proteomics

Université Aix Marseille I

Uppsala University

Pedro´s Biomolecular Research Tools. University of Dusseldorf.

Bioinformatics.ca (NAR, 2005)

Bionanotechnology.cl

Genesilico.pl

George Georgiu Lab

David Baker Lab

York Structural Biology Laboratory

Biocatalogue

The Lab Rat


Jobs

Science Jobs, Postdoc Search...

 


Intergenomics Group - Prof. Fernando de la Cruz Laboratory
. Molecular Biology Department. School of Medicine. Universidad de Cantabria & Instituto de Biomedicina y Biotecnología de Cantabria.
Avenida Cardenal Herrera Oria, s/n 39011 Santander (Spain). Tel. +34 942 201944 | Stats | Analytics