Computer Information
Core Laboratory Methods

Crystallography

Synchrotrons

Protein/Nucleic Acid Databases & Tools

Chemistry

Journals

Grants Information

Life Sciences Companies

Organizations

Other Useful Sites

Computer Information

 

· Core Laboratory computer links

 

Core Laboratory Methods

 

· Crystallization Screens Available to the Lab

· Expression of a selenomethionine variant in E. coli

· General molecular biology methods

 

Crystallography

Crystallization

· BMCD  Biological Macromolecule Crystallization Database

· CRYSTOOL  Computing of efficient screening conditions

· Emerald Biostructures  Crystallization products

· Hampton Research  Crystallization products

 

Data Processing

 

· CrystalClear GUI for data collection and processing based on d*TREK

· Crystal Twinning Server  Merohedral Twin Detector: Padilla-Yeates Algorithm

· HKL Package  Denzo/Scalepack

· MOSFLM  Data processing package

 

Phasing Packages

 

· CCP4  Collaborative Computational Project, Number 4 (software suite)

· CNS  Crystallography & NMR System

· Phases  Package of computer programs designed to compute phase angles for diffraction data from macromolecular crystals

· PHENIX  Python-based Hierarchical ENvironment for Integrated Xtallography

· REPLACE  Molecular replacement package

· SHARP  Statistical Heavy Atom Refinement and Phasing, includes density modification and auto-tracing

· Shelx  Software suite for heavy atom location and high-resolution refinement

· Shake-and-Bake  Dual-space direct-methods procedure for determining crystal structures

· SOLVE  Automated crystallographic structure solution for MIR, SAD, and MAD

· X-PLOR  Structure determination and refinement

· XtalView  Crystallographic software package for fitting electron density maps and solving structures by MIR and MAD

 

Refinement 

· Bias Removal Server  Bias removal and map improvement

· CCP4  Collaborative Computational Project, Number 4 (software suite)

· CNS  Crystallography & NMR System

· PHENIX  Python-based Hierarchical ENvironment for Integrated Xtallography

· Shelx  Software suite for heavy atom location, phasing, and high-resolution refinement

· TNT  Least-squares structure refinement

· X-PLOR  Structure determination and refinement

 

Structure Modeling

 

· BobScript  MolScript with electron density functionality

· Coot  Model building with real-space fitting

· GLR  Graphical interface integrating Bob/MolScript, Raster3d, and POV-Ray for generation of figures

· Hic-Up Server  Database of ligand, co-factor, etc. coordinates and topology files for O, CNS, X-PLOR, TNT

· MolScript  Creates both detailed and schematic pictures of molecular 3D structures, in particular proteins

· O  Model building

· PRODRG Server  Converts coordinates for small molecules in PDB format to the following topology formats: GROMOS, GROMACS, WHAT IF, CNS, O, SHELX, HEX and MOL2

· PyMOL   Molecular modeling system

· RasMol  Model viewer

· VMD  Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting

· XtalView  Model building (Xfit program)

 

Structure Analysis

 

· Domain Movement  Detects the domain movement from two homologous protein structures

· GRASP  Display and manipulation of the surfaces of molecules and their electrostatic properties

· PARVATI  Protein Anisotropic Refinement Validation and Analysis Tool

· PDB Structure Validation Server

· Richardsons' Validation Tools  MolProbity

· SAVS  Structure Analysis and Verification Server

· STAN  Structure Analysis Server

· Uppsala Software Factory  Various crystallographic tools

· WHATCHECK  Structure validation

 

Tutorials

 

· Bart Hazes' Tutorials on Data Collection, Heavy Atom Binding, Molecular Replacement

· Crystallography 101

· Fourier Transform

· MAD Phasing  Ethan Merrit's Site

· MAD Phasing  Bernhard Rupp's Site

· Mike Sawaya's Tips

· Structure Factors

 

Synchrotrons

 

· ALS  Advanced Light Source

· APS  Advanced Photon Source

· CHESS  Cornell High Energy Synchrotron Source

· NSLS  National Synchrotron Light Source

· SSRL  Stanford Synchrotron Radiation Laboratory

 

Protein/Nucleic Acid Databases & Tools

 

· BCM launcher  Baylor College of Medicine Search Launcher

· BLAST  Basic Local Aligment Search tool

· BLAST2  Advanced Basic Local Aligment Search tool

· BLITZ  Sequence comparisons

· BLOCKS  Sequence comparisons

· DALI  Comparison of Protein Structures 3D

· EMBL European Molecular Biology Laboratory (Heidelberg)

· Entrez Molecular Biology Server

· ExPASy  Molecular Biology Server

· GenBank  Gene Database

· LIGIN  Molecular docking using surface complementarity

· MMDB  Molecular Modelling Database

· NCBI  National Center for Biotechnology Information

· PDB  Protein Data Bank (Rutgers)

· Pedro's Biomolecular Research Tools

· Predict Protein

· PSIpred  Protein Structure Prediction

· SCOP  Structural Classification of Proteins

· SSCP  Secondary Structure Content Prediction

· STRIDE  Protein secondary structure assignment from atomic coordinates

 

Chemistry

 

· Chemistry Links

· Resources in Chemistry

· Web-Elements

 

 

Journals

· Accounts of Chemical Research

· Acta Crystallographica

· Archives of Biochemistry and Biophysics

· Biochemistry

· Cell

· Journal of Bacteriology

· Journal of Biological Chemistry

· Journal of Molecular Biology

· Nature

· Nature Structural Biology

· Proceedings of the National Academy of Sciences

· Protein Science

· Proteins: Structure, Function, and Genetics

· Science

 

Grants Information

· ALS Association

· American Federation for Aging Research

· GrantsNet

· NIH

· NSF

· The Welch Foundation

 

Life Sciences Companies

· Aldrich/Sigma

· American Type Culture Collection

· Amersham Pharmacia Biotech

· Applied Biosystems

· Boehringer-Mannheim (Roche Molecular Biochemicals)

· Clontech Labs

· DNA transfection products

· Emerald Biostructures

· Eppendorf Scientific Inc.

· Fisher Scientific

· Hampton Research

· Integrated DNA technologies

· Invitrogen Corp.

· Life Technologies

· Midland Certified Reagent

· Molecular Dynamics

· Novagen Inc.

· Olympus America Inc.

· Perkin-Elmer

· Promega Corp.

· Protein Solutions

· Sigma/Aldrich

· Stratagene Cloning Systems

· VWR

 

Organizations

· The ALS Online Database for Mutations in ALS Related Genes (alsod.org)

· American Crystallograhic Association

· International Consortium on Superoxide Dismutase and Amyotrophic Lateral Sclerosis

· International Union of Crystallography

· Mycobacterium tuberculosis Structural Genomics Consortium

· Southwest Macromolecular Symposium

· West Coast Protein Crystallography Workshop

 

 

Other Useful Sites

· Andrew Hinck Lab Page

· Lesa Beamer Lab Page

· Jon Robertus Lab Page

· UCLA-DOE Lab Page

· UTHSCSA Biochemistry Web Page

Science Links