Links
Seminars:
- Protein Structure Club
- BME 281R: E2 577, Tues 12:30-2pm
- MCD seminars
- Chemistry seminars
- CBSE seminars
- SOE seminars
- BME 280B
- Bay Area Bioinformatics
Literature:
- Journals
- PubMed
- Web of Science
- UCSC Electronic Journals
Online Books and Courses:
- Durbin and Eddy errata
- O'Reilly Network Safari Bookshelf
- Wiley InterScience :: Collection
- Protein Structure and Function Petsko and Ringe
- An Introduction to Computational Biochemistry Tsai
- Bioinformatics and Functional Genomics, Pevsner
- Bioinformatics, Baxevanis and Ouellette
- Bioinformatics For Dummies Claverie and Notredame
- Introduction to Protein Structure
- Principles of Protein Structure
Link Pages:
- Bioinformatics - UCSC Science & Engineering Library
- Guide to Selected Bioinformatics Internet Resources, from Issues in Science and Technology Librarianship
- CMS Molecular Biology Resources
- Pedro's Biomolecular Research Tools
- Sali Lab Links to Modeling Tools
Protein Sequence Analysis:
- ExPASy
- EBI
- NCBI
- PredictProtein
- PIR
Secondary Structure Prediction:
- PhD
- SAM-T02
- Psipred
Protein Domains/Families/Motifs:
- CDD
- InterPro
- Pfam
- ProSite
- TIGRFAMs
- SMART
- BLOCKS
- ProDom
- SBase
- PINTS
Protein Function and Interaction:
- DIP Database of Interacting Proteins
- BIND Biomolecular Interaction Network Database
- KEGG
- ENZYME
- Evolutionary Trace Server
- ConSurf
- Database of Macromolecular Movements
- Rosetta Domain Fusion Analysis
Alignment Tools:
- WebLogo
- JalView
- T-coffee (dowload)
- Clustal-W
- MUSCLE
Protein Structure:
- Protein Data Bank
- amino acids
- IUPAC nomenclature
- pdb file format
- Pisces
- ASTRAL
- SCOP
- CATH
- FSSP
- DALI Domain Dictionary
- SPIN-PP interfaces
- TOPS
Molecular Rendering:
- Rasmol Manual
- PyMOL
- Swiss-PDB Viewer
- Chimera User's Guide
- Molscript
- CN3D
- Chime Mac and Windows only
- Raster3D
- MolMol contact maps
- O
- MAGE and KineMAGE
Structure Validation & Analysis:
- Biotech server WhatCheck and Procheck
- RCSB List of Software
- LLNL Prediction Center
- Anolea
- Prosa
- Procheck
- Verify3D
- GRASS
- MolProbity
- Probe
- Tools from the Richardsons
- Verfiy3D
- VADAR Volume, Area, Dihedral Angle Reporter
- UCSF Software DMS (molecular surfaces) KSDSSP (secondary structure)
- WhatCheck
- SurfaceRacer
- DSSP web interface
- DSSP
- STRIDE
- STING Millenium
-
Structure-Structure Comparison:
- LGA
- EBI DALI server
- DaliLite
- CE
- Mammoth
- ProFit
- VAST
Fold Recognition and Alignment:
- BAliBASE benchmark alignments
- bioinfo.pl Meta Server Submits a sequence to many fold recognition servers
- HMM-based Protein Structure Prediction, SAM-T02
- GenThreader
- Prediction Center Links fold recognition servers
Protein Modeling and Structure Prediction:
- AL2TS
- Swiss-Model
- What If
- 3D-JIGSAW Protein Comparative Modelling Server
- ModBase
- ModWeb: Comparative Modeling Server: Ver.0
- Modeller
- Robetta Fragment Server
- HMMSTR/I-sites/Rosetta
- Dunbrack's Sidechain page rotamer libraries, analysis and modeling
- Dunbrack rotamer libraries
- SCWRL3
- CHARMm
- AMBER
- GROMOS
- Tinker
- FTDock
- AutoDock
Structure Prediction Evaluations:
- CASP
- CAFASP
- LiveBench
- EVA
Experimental Structure Determination:
- Lawrence Livermore's crystallography tutorial
- MRC crystallography course
- Max Planck NMR tutorial
- BioMagResBank
- CNS
- O
Homepages:
- UCSC CompBio
- David Baker
- Chris Bystroff
- Michael Levitt
- Mark Gerstein
- Ram Samudrala
- Jane Richardson
- Rob Russell
- Barry Honig
- Jay Ponder
- David Jones
- Roland Dunbrack
Miscellaneous:
- GIST: Support Vector Machine Beta 1.0