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Useful links

On this page:
Modeling
   Homology modeling
   Fold recognition
   Membrane proteins
   Education in molecular modeling
   Other links

Databeses

Multifunctional portals

Scientific software

Chemical resources
   CD spectra analysis
   Theoretical chemistry

Genome

Other links

Bibliography
   Journals" websites
   Links
   Various
   Textbooks online

Homology modeling

• MODELLER - A program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. (A. Sali);
• ModBase (A. Sali);
• Protein structure prediction at Scripps;
• JACKAL (A Protein Structure Modeling Package);
• Consensus.

Fold recognition

• SnapDRAGON (domain boundary prediction);
• UCLA-DOE server;
• Prospect (PROtein Structure Prediction and Evaluation Computer Toolkit).
• PSIPRED Protein Structure Prediction Server (D. Jones);

Membrane Proteins

• Membrane proteins with known 3D-structure;
• Structure Prediction of Membrane Proteins (links);
• T. Woolf"s group;
• D. Engelman group (Yale);
• P. Tieleman"s site;
• M. Sansom"s home page;
• Lipiddock (Stewart, UK);
• POPC bilayer (Heller);
• Structure of membranes (textbook);
• LIPIDAT (database).

Education in molecular modeling

• Yale MolMod course;
• Bioinformatics - Training courses;
• Guide to protein structure prediction;
• Molmod tutorial (Utrecht);
• Proinformatics (3D, video);
• Computational Tools For Protein Modeling;
• Molecular Monte Carlo;
• BIO - figures (misc);
• Biophysics Textbook On-Line;
• Forces in proteins (textbook);
• Protein Physics by A.V. Finkelstein;
• MolMod group, Imperial College, London (Molecular Modelling for Organic Chemistry);
• See all textbooks list.

Other links

• ANTAS-AGRARIA (MolMod);

  MD Salon;

  Molecular Graphics Laboratory, Scripps Res. Inst.;

  Sutcliffe group (Clustering An Ensemble Of NMR-Derived Protein Structures Into Conformationally-Related Subfamilies);

  Molecular Modeling at Scripps;

  Scheraga"s soft (Computational biology service unit);

  Open Science (bioinformatics).

• Databases on lipids, proteins etc. (links);
• Biological databases (NAR-2001);
• ENTREZ - protein retrieve system;
• PDB;
• SWISS-PROT;
• Protein Sidechain Conformational Analysis (ROTAMER library);
• GPCRDB (Information system for G protein-coupled receptors (GPCRs));
• Computational Chemistry Comparison & Benchmark DataBase;
• Reaction Citation Index;

• Structural Biology Software Database;
• CHEMISTRY software database);
• CompuChem software;
• Accelrys;
• ExPASy proteomic tools;
• Practical Molecular Biology (RU);
• Russian Molecular Biology server;
• EMBNet services;
• Sequence Analysis Tools (Canada);
• GENEBEE services;

• Software from D.J. Wales;
• HINT (Hydropathic INTeractions);
• Q (Molecular dynamics);
• CEMCO soft (MCPRO, BOSS, etc.);
• Direct FF;
• MODELLER-6;
• CAST - cavities in proteins;
• PyMOL;
• SC: measuring shape complementarity at protein-protein interfaces;
• CPMD - quantum MD;
• FLEXX;
• COLUMBUS (quantum chem. programs);
• Chime (MDL);
• NACCESS;
• BOSS 4.1 manual (PDF)
• SURFNET;
• WEBMO;
• ECEPPAK (NIH);
• MMTK - Mol. Mod. Toolkit;
• Ghemical (Mol. Mod. soft);
• VEGA;
• MOLSURF;
• GROMOS;
• GROMOS96;
• FANTOM;
• GROMACS-3.0;
• DOCK-4.0;
• GOLD;
• BioCore: NAMD, VMD..;
• DSSP;
• Top Pred 2;
• MOPAC manual;
• GCG help on-line;
• SPROUT 4.3 (de novo ligand design);
• CONCORD modeller.
• Scheraga"s soft (Computational biology service unit);
• J. Ponder"s page (Tinker);

• Organic chemistry resources;

CD spectra analisys

• DICHROWEB (On Line Circular Dichroism Analysis);
• CD-PRO (A Software Package for Analyzing Protein CD Spectra);
• K2D (Prediction of percentages of protein secondary structure from CD spectra).

Theoretical chemistry

• Quantum Chemistry Literature Database (QCLD);
• MOLCAS (q. chem.);
• MOLPRO (q. chem.);
• W. Jorgensen group;
• JAGUAR 4.1 manual.

• Computing the genome;
• Genome - images;
• Protein sequence analysis;
• PSIpred (Prediction of secondary structure from multiple sequences);
• Structural Genomics (NIGMS);
• Functional genomics.

• Biolinks;
• Chemistry, Biology and related soft - many links;
• Computational Biochemistry & Biophysics (links);

Journals" websites

• SCIENCE Online;
• Nature genomics;
• Nature Structural Biology (for authors);
• NATURE physcics;
• Elsevier-Physics;
• FEBS Letters;
• Molecules;
• Proteins;
• Protein Science;
• Journal of Biological Chemistry;
• Journal of Molecular Biology;
• European Journal of Biochemistry;
• JBSD (Jouranal of Biomolecular Structure and Dynamics);
• Biochemical Journal;
• Journal of Computational Chemistry;
• Biopolymers;
• J. Bioenerg. Biomemb.;
• Journal of Experimental Medicine;
• EMBO Journal;
• International Journal of Molecular Science;
• Journal of Virology;
• TCA (Theoretical Chemistry Account);
• Biochemistry;
• Journal of Physical Chemistry;
• Biophysical Journal;
• JACS;
• Current Opinion in Structural Biology;
• Current Medicinal Chemistry;
• Internet Journal of Chemistry;
• Journal of Molecular Graphics & Modeling;
• VJB (Virtual Journal of Biophysics);
• Journal of Theoretical Computational Chemistry;
• Journal of Computer-Aided Molecular Design;
• European Journal of Medicinal Chemistry.

Links

• Chemistry Journals;
• Wiley - Interscience;
• Oxford University Press;
• MAIK - NAUKA;
• Nauka i zhizh";
• Web sites: chemistry (links);
• Pub Med Central initiative.

Various

• Scientific writing (recomendations);
• The Scientific World;
• Belstein abstracts database;
• Bookstore (Computational chemistry);
• AMADEO (Med. lit. service);
• SCIRUS - scientific search engine;
• Foundations of Chemistry;
• BIONET archives.

Textbooks online

• R. Feynman (The character of physical laws);
• Structure of membranes (textbook);
• Biophysics Textbook On-Line;
• Forces in proteins (textbook);
• Protein Physics by A.V. Finkelstein;
• Molecular dynamics (I);
• Molecular dynamics (II);
• Numerical Recipes in Fortran;

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