Mike's Links

Based on the centuries old concept of tangled webs, here is a mostly disorganized collection of links that I hope you find interesting, useful or even enjoyable.


Membranes

    Experimental groups working on membranes:

Steve White's group at UC Irvine.  Among other cool things, they do high resolution neutron and X-ray scattering studies of fluid lipid bilayers
John Naggle's group at CMU.  They do X-ray scattering of membranes.
Klaus Gawrish at the NIH. He does NMR studies of membranes and membrane interfaces.
Adrian Parsegian's group at the NIH. They do osmotic stress measurement to understand the forces between biomolecules.
    Theoretical groups working on membranes:
Max Berkowitz's group at UNC.
Scott Feller at Wabash College.
Eric Jacobbson at UIUC.
Mike Klein's group at Penn.
Mark Sansom's group at Oxford.

disclaimer: there are probably hunderds of groups around the world working on membranes, and there are probably 105 papers published every year on membranes and related subjects. I am able to read far fewer than that and, unfortunately, understand even less. So don't be annoyed or dismayed that I missed you or your favorite links.

Literature
Biophysical Journal
Chemistry journals
HighWire Press
Biological Journals and Abbreviations: Title Page
Nature - International weekly journal of science
Stanford University Libraries
Journal of Computational Biology
ICARUS, International Journal of Solar System Studies
Internet Journal of Chemistry
General Pharmacology
Nature Structural Biology
Proceedings of the National Academy of Sciences

The Journal of Chemical Physics
 
Computational Chemistry
Are still in the disoganized mess, part of which is appended below...
Other stuff about me
I grew up in Huntington, WV, home of Marshall University.
I was an undergraduate at MIT and lived in Senior House.
I did my graduate work in Chemistry at UC Berkeley, with Lawrence Pratt, who is now at Los Alamos.
I did a postdoc with David Chandler, who is still at UC Berkeley.
I am currently at UC San Francisco, in the Department of Pharmaceutical Chemistry.
I spend most of my time in the Exobiology Branch at NASA Ames Research Center.
We get a lot of our computational support from the  NAS Systems Division here at Ames.

Saxophones and other music related links (one of these days I'm going to set up a web page from home). Until then...

Mel Martin's web site is an amazing compendium of links pertaining to sax, flute, clarinet, jazz and music in general.
Sax on the Web has a fine collection of articles about saxophones and a lively discussion board.
The clarinet pages have a huge collection of articles about clarinets as well as a discussion board.
While in grad school, I was a member of the UC Jazz Ensembles.
Susan Muscarella, a former director of UCJE, has founded the Jazz School, in Berkeley,
where old friends and teachers Bill Aron and Dave LeFebvre do some teaching.
And if you must play bass clarinet, for whatever reason, you need to find a place to do so. I do it in the Contra Costa Wind Symphony.


A bunch of  not-so-well-organized  bookmarks:

Proteins

Brooks Group Home Page
Crystallography 101
Entrez Browser
The RCSB Protein Data Bank
The National Center for Biotechnology Information
Computational Biology Services
Biology WorkBench (tm)
CCL: Summary: Topological indices and active sites

Coiled-Coils

Fibritin of Bacteriophage T4
Coiled Coils
Protein Structures - Peter S. Kim Lab - Whitehead Institute / MIT

Ion Channels

gopher://gopher.nih.gov/77/gopherlib/indices/pir/index?GABA
Laboratory of S. John Mihic, Ph.D.
The Ion Channel Network (ICN) Home Page
Ligand Gated Ion Channel database
Ion channel mutations database: Home

PNA's

Peptide Nucleic Acid (PNA) Jump Station
Applied Biosystems: PNA Website
PNA
Applied Biosystems: PNA: Bibliography
BPI PNA Publications
Introduction
PNA-entrez lit search 1 12-Sep-00
Home Page of the Center for Biomolecular Recognition

Protein Folding

Structure Prediction and Evaluation
Strategic Simulation Initiative: Computational Structural Biology

Recognition

Ghadiri Group Home Page

Simulations

Pfam : Home page (St. Louis)
CBS home page
Antimicrobial Peptides and Proteins - Literature
New EBI Home Page
NDB Archives
Gregory A. Petsko
Henry Lester and Norman Davidson
Medicine Related Bookmarks
The PredictProtein server
Infoseek: Results
Yale Molecular Biophysics Biochemistry Center Structural Biology
The National Center for Biotechnology Information
Pedro's BioMolecular Research Tools
Super Chemistry and Biology Links
Secondary Structure Prediction
The Generation and Use of Large 3D Databases in Drug Discovery
Genamics SoftwareSeek - Molecular Biology and Biochemistry Software Database
PhRMA Foundation
Phylogeny Programs
DNA / Protein
Lab of George Humpf

Chemistry

Nanoscale and Material Science
The van Gunsteren group's home page
Hexagonal ice
Water structure, behavior and properties: an explanation
Molecular Library
Molecular Mechanics and Force Field References
CCLMS - Research Title
Molecular Modelling Toolkit
ChemWeb Member Home Page
Other sites: LIPIDAT 1.0 WWW (c) 1996 OSURF
Glycerolipid Homepage
Chemistry Molecular Models
ACS Division of Physical Chemistry
MSCI XMol Manual Page
Rayshade Homepage
Molecular Simulations Inc.
The CMM Home Page
RasMol 2.5
AMBER
http://www.amber.ucsf.edu/amber/ff94/parm96.dat
Computational Chemistry List Home
ff_evaluation_suite
The GROMOS home page
Cambridge Crystallographic Data Centre
Molecules from Chemistry at Okanagan University College: Acids

Bioinformatics

MBGD Microbial Genome Database
Microarray Software
Clustering Program
Human Genome - EST Clustering Databases
Background

Services

SAS alignment
Submit Domain PD001990 (ProDom 99.2) to PredictProtein (advanced)
The Protein Machine
GENSCAN Web Server
Zürich University, Department of Biochemistry
3DPSSM Server
SWISS-MODEL
MEME - Submission form
MAST - Submission form
Weizmann
Biology WorkBench (tm)
UCSC HMM Applications Main Page

Resources&Manuals

BLAST

http://www.cgr.ki.se/cgr/groups/sonnhammer/Belvu.html
WU-BLAST 2.0 Description
WU-BLAST Archives
BLAST 2.0 Release Notes
BLAST Reference Manual Pages

CLUSTAL

ClustalW

DOCK

DOCK WWW Page

FASTA

Biochemistry Research - Pearson
fasta.html
Fasta Page

FILE FORMATS

File Format Standards
Stockholm format

GEANFAMMER

Geanfammer home page : genome analysis and protein family maker

HMMER

HMMER 2.1 User's Guide

HMMPRO

Net-ID, Inc: Bioinformatics and Data Mining

JALVIEW

JalView - Java alignment editor

MEME/MAST

MEME - Introduction
MAST - Introduction
MEME - Introduction

metaMEME

Meta-MEME v2.0.1
MEME - Introduction

MINI-SQL

Hughes Technologies : The home of Mini SQL ( mSQL )

PERL

Perl Paraphernalia: Understand References Today
bio.perl.org - Main page
Rex Swain's HTMLified Perl 5 Reference Guide
PERL.COM - Current Issue
82.562: Perl Patterns
82.562: Perl Tutorial
Perl Tutorial
Perl tutorial: Start

PHYLIP

PHYLIP Home Page

PRATT

Pratt Project Main Page
Pratt

RDB

RDB commercial

SAM

SAM: Sequence Alignment and Modeling System
Dirichlet Mixtures and other Regularizers
Computational Biology at Sandia National Laboratories
Barton Group Software
http://www.mrc-lmb.cam.ac.uk:80/genomes/GJM/bootstrap.html
Computational Biosciences at Oak Ridge National Lab
IBC Home Page
ISCB Training information
Bioinformatics Course Genome Resources Page
Phylogeny Programs
Laboratory of Computational Genomics : Services : Links
The Sanger Centre : Informatics Software: Wise2

Articles

The phylogeny of HIV
Phylogeny and reconstructing phylogenetic trees
Irish Database Course
Comprehensive Relational Course
White Papers - The Fundamental Principles for Constructing a Successful Biological Laboratory Informatics System

Databases

Virtual lab for biologists
SAWTED Web Server
PROTEIN FOLD RECOGNITION SEQUENCE INPUT FORM
NCBI Taxonomy Homepage
Proteome Databases Home Page
Sequences Annotated by Structure
SCOP: Structural Classification of Proteins
UCL-CATH prot. domains
PDBsum
UCL Biochemistry Protein Analysis & Modelling
CATH structure classify
NPS@ (proscan, etc)
EMBL Outstation, Hinxton. - Tools Home
Ligand Gated Ion Channel database
The Tree of Life Home Page
ICGEB: SBASE web server
LPFC: A Library of Protein Family Cores
The ProDom protein domain database
Protein Kinase Resource
The Ion Channel Network (ICN) Home Page
TreeBASE
Ribosomal Database Project II
NCBI
3D Drug Structure Databank
NEW PDB
Protein Databases
Entrez Browser
ExPASy Molecular Biology Server
Blocks WWW Server
HSSP database
Pfam : Home page (St. Louis)
The Institute for Genomic Research

Origins

Introduction to Evolutionary Biology
MISSION 2004 (12.000): Home
Geology 105: History of Life
Exploring Earth's Extremes Website
Introduction to the Archaea
The Diversity of Metabolism in Procaryotes
The Tree of Life Home Page

Protein Graphics

XMakemol Homepage
PyMOL Home Page
VMD - Visual Molecular Dynamics
MOLMOL - MOLecule analysis and MOLecule display
Raster3D (photorealistic molecular graphics)
X-PLOR Resources
RasMol Home Page
MolScript v2.1: Documentation

Communications

PuTTY: a free Win32 telnet/ssh client
The Kermit Project - Columbia University
Metro State's SSH (MSSH)
Jonas Walldén: NiftyTelnet 1.1 SSH

Compilers

Catalog of compilers: m4
Absoft Corporation Home Page

N-Body codes

Welcome to GROMACS
CS267: Notes for Lecture 25, Apr 16 1996
N-Body/Particle Simulation Methods
Scientific Computations Group Home Page
NAMD - Scalable Molecular Dynamics
A GENERAL-PURPOSE MD CODE

Fortran

ftnchek, A static analyzer for Fortran 77
Table of Contents
The Apache Software Foundation
Hashing
PVM: Parallel Virtual Machine
Babel manual
SGI Freeware Alphabetical Index
VMS page
MacInTouch: Mac news, information and analysis
Sizzling HTML Jalfrezi - HTML by Example
Numerical Integration: Gaussian Quadratures
Computational Physics Resource on the Internet
JUDEA PEARL'S HOMEPAGE
Peta Computing Institute.Ltd.
WinEdt
MMTK Home Page
PrestoPlot
Bilayer
Peta Computing Institute.Ltd.