Dominguez Lab

BBRI WEBMAIL

Molecular Biology

EMBL European Molecular Biology Server
UniProt Universal protein resource
ExPASy Proteomics Server
NDB Nucleic acid data base
NCBI National Center for Biotechnology Information, USA
ACGT Advanced Center for Genome Technology at University of Oklahoma, USA
TIGR The Institute for Genomic Research,USA

Protein Sequence and Structure Analysis

PDB Protein Data Bank
PredictProtein Sequence analysis, and structure prediction
Clustal W Multiple sequence alignment
T-COFFEE Multiple sequence alignment
ESPript Multiple sequence alignment
Muscle Protein multiple sequence alignment software
Inub A fold-recognition server, search for compatible three-dimensional structures
HCA Hydrophobic cluster analysis
DisEMBL Intrinsic protein disorder prediction
DISOPRED2 Prediction of protein disorder server
FoldIndex predict whether a given protein sequence is intrinsically unfolded
POPMUSIC Prediction Proteins Mutations Stability Changes
Paircoil Coiled-coil prediction software
Cambridge Database Database of Protein Alignments organised as Structural Superfamilies
EBI European Bioinformatics Institute, UK
PIR Protein Information Resource at National Biomedical Research Foundation, USA
Pole Bio-Informatique Lyonnais Sequence Analysis
VAST Search for structural homologues
CATH Class, Architecture, Topology, Homology Database
CCDC Cambridge Crystallographic Data Centre, a searchable database of organic and metallo-organic crystal structures
HSSP Database of homology-derived secondary structure of proteins
CCMS Computational Center for MacroMolecular Structures
BCM Search Launcher Six Frame Translation of Sequence
The Sequence Manipulation Suite

Crystallography Software and Databases

BMM Biomolecular modelling software collection
BUSTER Software system for crystallographic structure determination
CCP4 Collection of disparate programs covering most of the computations required for macromolecular crystallography
HKL High quality software and hardware solutions for X-ray crystallography laboratories and synchrotron beam lines.
MOLSCRIPT Program for displaying molecular 3D structures
GRASP Molecular visualization and analysis program
POV-Ray Free tool for creating stunning three-dimensional graphics
RASTER 3D Set of tools for generating high quality raster images of proteins or other molecules
RASMOL Software for looking at macromolecular structure
O Source of general purpose macromolecular modelling environment
PROCHECK Programs to check the Stereochemical Quality of Protein Structures
DALI Search for structural homologues
MSD Protein structure matching
CNS Flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination
X-PLOR 3D structure determination of macromolecules using crystallographic diffraction or NMR data
MOLMOL Display, manipulation, mutation and editing of molecular data-files
SnB Determining crystal structures from X-ray diffraction data
SOLVE Automated crystallographic structure solution
UPPSALA Software and Resources for Macromolecular Crystallography and Structural Biology
PYMOL High-quality molecular graphics
ICM Programs for molecular modeling, bioinformatics, cheminformatics and docking
SHELX Set of programs for crystal structure determination
BMCD Biological Macromolecule Crystallization Database
Heavy-Atom Databank HEAVY-ATOM derivatives of protein crystals
X-ray absorption edges Elements characteristic x-ray absorption edge energies
WebElements 2 Periodic table at Sheffield, England
ACA American Crystallographic Association
ReLiBase Receptor/ligand complex database (JAVA search)
Coot Model building tool for molecular graphics

Synchrotrons

APS Argonne National Laboratory (Chicago, Illinois, USA)
BioCARS Synchrotron structural biology resource (Chicago, Illinois, USA)
IMCA-CAT Industrial macromolecular crystallography associacion collaborative access team (Chicago, Illinois, USA)
Photon Factory Structural biology research center (KEK, Tusukuba, Japan)
National Synchrotron Light Source National user research facility (Brookhaven, NY USA)
CHESS High-intensity high-energy X-ray synchrotron source, Cornell Univ. (Ithaca, NY USA)
ESRF European Synchrotron Radiation Facility (Grenoble, France)
Daresbury CCLRC Daresbury Laboratory (Daresbury, England)

X-ray Hardware and Crystallization Tools

MARResearch X-ray detectors

OXFORD Cryosystems

RIGAKU X-ray generators

Hampton Research - Crystallization solutions and tools

Nextal - Crystallization solutions

Granting Agencies

NIH National Institute of Health
NSF National Science Fundation
American Heart Assiciation National health agency for reducing disability and death from cardiovascular diseases and stroke
March of Dimes Mission of the March of Dimes is to improve the health of babies by preventing birth defects and infant mortality
GrantsNet Resource to find funds for training in the sciences and undergraduate science education