Perform Computations

Topic Web Site Link Description Author of Web Site

Protein Modeling DALI Compare protein structures L. Holm, EMBL

GCG-Lite Protein sequence analysis tools P. FitzGerald, NIH

MMTSB Multiscale Modeling Tools in Structural Biology Scripps Research Institute

nnpredict Secondary structure prediction (neural net-based) D. Kneller, UCSF

PredictProtein Secondary structure prediction (including transmembrane helices) and solvent accessibility B. Rost, EMBL

Quadratic Logistic Algorithm with and without homologues Secondary structure prediction P. Munson, NIH

SARF Spatial Arrangement of backbone fragments N.N. Alexandrov, Laboratory of Mathematical Biology, NCI

Swiss-Model Automated Protein Modeling Server Manual C. Peitsch, Glaxo Institute of Molecular Biology, Geneva

TMAP Secondary structure prediction of transmembrane segments B. Persson, EMBL

WAM Antibody Modeling on the Web T. Rees, Bath University

Topic	Web Site Link	Description	Author of Web Site
Protein Modeling	DALI	Compare protein structures	L. Holm, EMBL
GCG-Lite	Protein sequence analysis tools	P. FitzGerald, NIH
MMTSB	Multiscale Modeling Tools in Structural Biology	Scripps Research Institute
nnpredict	Secondary structure prediction (neural net-based)	D. Kneller, UCSF
PredictProtein	Secondary structure prediction (including transmembrane helices) and solvent accessibility	B. Rost, EMBL
Quadratic Logistic Algorithm with and without homologues	Secondary structure prediction	P. Munson, NIH
SARF	Spatial Arrangement of backbone fragments	N.N. Alexandrov, Laboratory of Mathematical Biology, NCI
Swiss-Model	Automated Protein Modeling Server	Manual C. Peitsch, Glaxo Institute of Molecular Biology, Geneva
TMAP	Secondary structure prediction of transmembrane segments	B. Persson, EMBL
WAM	Antibody Modeling on the Web	T. Rees, Bath University

Topic Web Site Link Author of Web Site

Three-dimensional Structures Crystallographic Symmetry Tool Univ. of British Columbia, Canada

G-Protein Coupled Receptor Database: 3D Models G. Vriend, EMBL

Phospholipid membrane models H. Heller, Ludwig Maximilians University, Munich

Protein Kinases Phil Bourne, San Diego Supercomputer Center

Protein Models generated using the program FOLD F.E. Cohen, UCSF

Protein Properties Amino Acid Structures and Properties V. Heinau & B. Kirste, Freie Universitat, Berlin

Atlas of Side Chain Interactions R. Laskowski, Univ. College London

Atlas of Side Chain and Main Chain Hydrogen Bonding I. McDonald and J.M. Thornton, Univ. College London

Backbone-Dependent Rotamer Library R.L. Dunbrack, Jr., UCSF

BioMagResBank, a database of NMR-derived protein information E. Ulrich, Univ. of Wisconsin

Conformations and solvent accessibilities of Residues in Protein Databank (PDB) proteins Washington Univ.

DSSP Databases C. Sander, EMBL

Proteins Motions Database M. Gerstein, Stanford Univ.

Chemical Data Web Elements M. Winter, Univ. of Sheffield

Molecular Properties Search the MedChem Database, containing log P, pKa, and other information for 26,000 compounds Daylight Chemical Information Systems, Inc.

Searchable QSAR database Biobyte

Topic	Web Site Link	Author of Web Site
Three-dimensional Structures	Crystallographic Symmetry Tool	Univ. of British Columbia, Canada
G-Protein Coupled Receptor Database: 3D Models	G. Vriend, EMBL
Phospholipid membrane models	H. Heller, Ludwig Maximilians University, Munich
Protein Kinases	Phil Bourne, San Diego Supercomputer Center
Protein Models generated using the program FOLD	F.E. Cohen, UCSF
Protein Properties	Amino Acid Structures and Properties	V. Heinau & B. Kirste, Freie Universitat, Berlin
Atlas of Side Chain Interactions	R. Laskowski, Univ. College London
Atlas of Side Chain and Main Chain Hydrogen Bonding	I. McDonald and J.M. Thornton, Univ. College London
Backbone-Dependent Rotamer Library	R.L. Dunbrack, Jr., UCSF
BioMagResBank, a database of NMR-derived protein information	E. Ulrich, Univ. of Wisconsin
Conformations and solvent accessibilities of Residues in Protein Databank (PDB) proteins	Washington Univ.
DSSP Databases	C. Sander, EMBL
Proteins Motions Database	M. Gerstein, Stanford Univ.
Chemical Data	Web Elements	M. Winter, Univ. of Sheffield
Molecular Properties	Search the MedChem Database, containing log P, pKa, and other information for 26,000 compounds	Daylight Chemical Information Systems, Inc.
Searchable QSAR database	Biobyte

Topic Web Site Link Author of Web Site

Software Molecular Modeling Software List Center for Molecular Modeling, CIT, NIH

Data/Parameters AMBER Parameters Department of Pharmacology, Institute of Medical Biology, School of Medicine, University of Tromsų, Norway

Quantum chemical basis sets Environmental Molecular Sciences Laboratory, Pacific Northwest Laboratory, Battelle Memorial Institute

Scripts HyperChem Script Library Hypercube, Inc.

Midas Scripts for Homology Modeling Scott Presnell, UCSF

SYBYL SPL Script Library Curt Breneman, RPI

SYBYL SPL Script Library The NIH Guide to Molecular Modeling