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Structural Biology Links Macromolecular Assemblages The Darst Laboratory Homepage http://www.rockefeller.edu/labheads/darst/index.html - studies structural aspects of bacterial transcription using Electron and X-ray Crystallography as well as Biochemical approaches. HHMI report on neurotransmission machinery http://www.hhmi.org/news/brunger.html - Mucking about with myosin motor mutants http://research.biology.arizona.edu/myosin/default.html - Making Myosin Mutants: an Approach to Understanding the Little Bitty Motor that moves you The myosin homepage http://www.mrc-lmb.cam.ac.uk/myosin/myosin.html - starting point for myosin information The Molecular Motors Group, University of York http://motility.york.ac.uk/ - uses single molecule techniques to investigate the mechanism of molecular motors. All the virology on the WWW http://www.virology.net/index.html - Excellent starting point for virology on the web World Index of Molecular Visualization Resources http://molvis.sdsc.edu/visres/ - a visitor-maintained collection of structural visualization resources Biological Macromolecule Crystallization Database and the NASA Archive for Protein Crystal Growth Data http://wwwbmcd.nist.gov:8080/bmcd/bmcd.html - crystal data and the crystallization conditions, which have been compiled from literature. These include proteins, protein:protein complexes, nucleic acid, nucleic acid:nucleic acid complexes, protein:nulceic acid complexes, and viruses. The SWI/SNF complex in Saccharomyces cerevisiae http://www.cmbi.kun.nl/edu/students/stages/finished/SWI-SNF/ The National Center for Macromolecular Imaging http://ncmi.bcm.tmc.edu/ncmi Photosystem I: X-ray structure analysis http://userpage.chemie.fu-berlin.de/~phosys/ - Photosystem I (PSI) is a large protein complex embedded within the photosynthetic thylakoid membrane. TRANSFAC http://transfac.gbf.de/TRANSFAC Membrane Protein Resources http://blanco.biomol.uci.edu/MemPro_resources.html Theory and Simulation [top] MDTools http://www.ks.uiuc.edu/Development/MDTools/ - a collection of programs, scripts, and utilities for researchers to make various modeling and simulation tasks easier, and to provide basic code and utilities which can be built up into larger toolsets. NAMD http://www.ks.uiuc.edu/Research/namd/ - parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology VMD: visual molecular dynamics http://www.ks.uiuc.edu/Research/vmd/ - a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting GAUSSIAN98 http://gears.aset.psu.edu/hpc/software/compchem/ - Gaussian 98 is designed to model a broad range of molecular systems under a variety of conditions performing its computations starting from the basic laws of quantum mechanics. Chemical dynamics resource at San Diego Supercomputer Center http://www.sdsc.edu/Software/chemistry.html - a series of programs for calculating chemical reactions, molecular modeling, and chemistry visualization. Dalton quantum chemistry program http://www.kjemi.uio.no/software/dalton/dalton.html - a powerful quantum chemistry program for the calculation of molecular properties with SCF, MP2, MCSCF or CC wave functions. Assisted model building with energy refinement (AMBER) http://amber.scripps.edu/ GROMACS http://www.gromacs.org/ - high performance system for simulating the Newtonian equations of motion for systems with hundreds to millions of particles. The Baker laboratory homepage http://depts.washington.edu/bakerpg/ Evaluating protein structure-prediction schemes using energy landscape theory http://www.research.ibm.com/journal/rd/453/eastwood.html Navigating protein–protein interfaces with MolSurfer http://www.embl-heidelberg.de/~gabdoull/ads/imap/ The ligand-gated ion channel database http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html The Bioinformatics Resource http://www.hgmp.mrc.ac.uk/CCP11/index.jsp ProStar — The Protein Potential Site http://prostar.carb.nist.gov/ The Biomolecular Interaction Network Database (BIND) http://bind.ca/ - a database designed to store full descriptions of interactions, molecular complexes and pathways. Human Genome [top] The human genome (Nature) http://www.nature.com/genomics/human/ - unrestricted access to the International Human Genome Sequencing Consortium’s draft of the human genome Celera publication site http://public.celera.com/index.cfm - a subscription-based, integrated research platform that provides online access to curated biological data |
