Lab:

protparam: weight, pI, extinction coefficient        http://web.expasy.org/protparam/

protein molar weight calculator  http://www.sciencegateway.org/tools/proteinmw.htm

on-line calculator of molecular weights http://www.labo.cz/mft/mol_vahy.htm

buffer calculator http://www.liv.ac.uk/buffers/buffercalc.html

periodic table http://www.webqc.org/periodictable-Calcium-Ca.html

molarity calculator https://britishpeptidelabs.com/molarity-calculator

Proteins:

Brenda-enzyme classification   http://www.brenda-enzymes.org/

About proteins and their structures: www.proteopedia.org

        1) sequence analysis

Uniprot protein sequence database   http://www.uniprot.org/

search only sequences with PDB structures       https://www.uniprot.org/blast/

NCBI sequence database    http://www.ncbi.nlm.nih.gov/

sequence from pdb https://proteiniq.io/app/pdb-to-fasta

protein calculator https://web.expasy.org/protparam/

glyco mass calculator https://www.nist.gov/static/glyco-mass-calc/

CLUSTALW: sequence alignment http://www.ebi.ac.uk/Tools/msa/clustalw2/

BLAST: find conserved domains in your sequence http://blast.ncbi.nlm.nih.gov/Blast.cgi

estimation of protein diameter: http://www.calctool.org/CALC/prof/bio/protein_size

EBI services http://www.ebi.ac.uk/

sequence alignement, output possible in pir format http://www.genome.jp/tools/clustalw/

glycosylation sites https://services.healthtech.dtu.dk/services/NetNGlyc-1.0/

        2) crystallization techniques, soaking

Setting up your crystallization plate    http://hamptonresearch.com/make_tray.aspx

        3) data processing and phasing

periodic table with X-ray properties  http://www.csrri.iit.edu/periodic-table.html

 Virtual Textbook of Organic Chemistry    http://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/cnvcalc.htm

        4) structure refinement and analysis

EBI-SSM: secondary structure matching http://www.ebi.ac.uk/msd-srv/ssm/

SSM using Dali server: http://ekhidna.biocenter.helsinki.fi/dali_server/

electrostatics more rigorously: PDB2PQR online   https://nbcr.net/pdb2pqr  and APBS http://www.poissonboltzmann.org/

 Validation: MolProbity http://molprobity.biochem.duke.edu/

Privateer glycans, carbohydrate validation https://privateer.york.ac.uk

Web services MUNI: http://webchem.ncbr.muni.cz/   (e.g. Patternquery .... PDB search)

Cavities and channels - Caver: http://www.caver.cz/

Mole: surfaces and caves (online) http://webchem.ncbr.muni.cz/Platform/App/Mole

         5) modelling tools

Swis-model  (homology modelling server) http://swissmodel.expasy.org/

Rosetta protein-protein docking: http://rosettadock.graylab.jhu.edu/ (server)

homology modelling program for download (paid) http://www.yasara.org

conserved surfaces:   http://consurf.tau.ac.il/

FoldX online http://foldxsuite.crg.eu/

        6) SAXS

Hamburg SAXS pages http://www.embl-hamburg.de/biosaxs

mass calculation Mowo http://www.if.sc.usp.br/~saxs/

Scatter    https://bl1231.als.lbl.gov/scatter/

Software overview   http://smallangle.org/content/software

DENsity from Solution Scattering web server  https://denss.ccr.buffalo.edu/

        7) IR and Raman spectroscopy

IR tutor http://www.columbia.edu/itc/chemistry/chem-c1403/ir_tutor/IRTUTOR.htm