Structure and function of biomolecules

Useful links

Formulatrix - crystal images in CMS: http://cms.ibt.biocev.org/RockMakerWeb/Login#/Projects

Bob wiki (internal) http://bob.imc.cas.cz/dokuwiki

CSSB (Czech Society for Structural Biology) http://www.structbio.org/

BIOCEV http://www.biocev.eu/

List of crystallographers http://www.weizmann.ac.il/esf_xtal/czech.html

Scientific projects running on home computers of volunteers http://boinc.berkeley.edu/

search in ASEP www.it.cas.cz/cs/lib/asep

RIV database http://www.isvav.cz/prepareResultForm.do

RIV database - new pages 2016: https://www.rvvi.cz/how to use ResearchID: http://www.lib.cas.cz/asep/pro-zpracovatele/researcherid/

ResearcherID http://www.researcherid.com

Czech crystallographers http://www.weizmann.ac.il/esf_xtal/czech.html

Časopisy:

časopisy přes knihovnu AV ČR: https://www.lib.cas.cz/eiz/vzdaleny-pristup/

časopisy - prehled přístupů: http://www.ibt.cas.cz/intranet/Provozni-zalezitosti/

journals of UMG, BTU http://sun2.biomed.cas.cz/fgu/knihovna/ecasopisy_komplet.html

journals of UMCH http://rzblx1.uni-regensburg.de/ezeit/index.phtml?bibid=IMC&colors=7&lang=en

knihovna areal http://sun2.biomed.cas.cz/fgu/knihovna/svi_fgu.html

www.suweco.cz -casopisy

Vestec:

http://www.perfectcanteen.cz/nase-provozy/perfect-canteen-biocev

http://www.restauracenablatech.cz

Areal of Krc:

map of Krc: http://www.biomed.cas.cz/areal_en.gif

Institutes in Krč http://www.biomed.cas.cz/indexcz.html

areál Krč (posilovna, mateřská školka, ubytovna) http://www.img.cas.cz/dalsi-zarizeni/VERSO www.eis.cas.cz odkazy->Praha->Verso, portal.ibt.cas.cz

http://www.eduroam.cz

http://pc15/backuppc/ zalohy (internal)

Ordinační hodiny MUDr Steppanové : 241062317, 2459 – tel.

po 7,30 – 12,30

út 7,30 – 12,30 13,00 – 15,00 (odpol. jen pro objednane)

st ----- 13,00 – 19,00

čt 7,30 – 12,30 13,00 – 15,00 (odpol. jen pro objednane)

pá 7,30 – 12,30

Technical support:

copy center Dejvice www.mpcopier.cz

colour labels for gases http://www.catp.cz/lahve.php

pravopisna prirucka http://prirucka.ujc.cas.cz

h-index (Hirschuv index): http://www.scopus.com/home.url

pdf editing online: http://www.pdfescape.com/

pdf merge online: http://online2pdf.com/ do 20 souboru celkem 50MB

pdf merge online: http://www.zamzar.com/ pdf konverze do 100 MB

webserver snadne formatovani referenci https://zbib.org/ ZoteroBib

Books and journals:

survey of journals available from IMC http://rzblx1.uni-regensburg.de/ezeit/index.phtml?bibid=IMC&colors=7&lang=en

Biomolecular Crystallography book (Bernhard Rupp) http://www.ruppweb.org/garland/default.htm

English explanatory dictionary: http://www.thefreedictionary.com/

Pišút, Gomolčák,Černý: Úvod do kvantovej mechaniky http://www.ddp.fmph.uniba.sk/pisut/qm/

X-ray data booklet http://xdb.lbl.gov/

časopis Bioprospect - bulletin Biotechnologické společnosti http://bts.vscht.cz/?q=node/19

Ewald: Fifty years of X-ray diffraction (online) http://www.iucr.org/publ/50yearsofxraydiffraction/full-text

Lectures:

Tenth National School on Neutron and X-ray Scattering 2008 http://neutrons.ornl.gov/conf/NXS2008/Present.shtml

Cheiron School 2010 http://cheiron2010.spring8.or.jp/lecture.html

molecular biology http://www.molbio.upol.cz/

Travelling:

travel connections in the world http://www.seat61.com/Linkspage.htm

plan travel by car: http://www.viamichelin.co.uk

maps of cities: http://mappery.com/

Unix:

cat and grep: http://www.robelle.com/smugbook/regexpr.html

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

how to determine protein concentration http://www-class.unl.edu/biochem/protein_assay/

weight -> moles for proteins http://molbiol.edu.ru/eng/scripts/h01_04.html

Proteins:

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

About proteins and their structures: www.proteopedia.org

Protein crystallography:

Summary: http://proteincrystallography.org/

A lot of software: http://en.bio-soft.net/

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 http://swift.cmbi.ru.nl/servers/html/soupir.html

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

protein calculator (Mw, pI, absorbance) http://www.scripps.edu/~cdputnam/protcalc.html

protein calculator (protein weight and molarity) http://molbiol.edu.ru/eng/scripts/h01_04.html

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

image of sequence with secondary structure: http://polyview.cchmc.org

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

protein calculator, eps280 and concentration http://www.mrc-lmb.cam.ac.uk/ms/methods/proteincalculator.html

conversion: weight - moles http://molbiol.edu.ru/eng/scripts/01_04.html

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

glycosylation sites http://www.cbs.dtu.dk/services/NetNGlyc/

2) crystallization techniques, soaking

heavy atom soaking http://exon.niaid.nih.gov/sis/cgi-bin/heavyatom_reactivity.cgi

heavy atom databank http://www.sbg.bio.ic.ac.uk/had/

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

similarity of crystallization screens: https://c6.csiro.au/login.asp

3) data processing and phasing

overview of synchrotrons and their parameters http://rcsb-biosync-beta.rutgers.edu/ new page http://biosync.sbkb.org/

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

plot f',f'' http://skuld.bmsc.washington.edu/scatter/AS_form.html

wavelength and energy conversion http://www.highpressurescience.com/onlinetools/conversion.html

http://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/cnvcalc.htm

adxv: software to display X-ray diffraction images http://www.scripps.edu/~arvai/adxv.html

Manfred Weiss: Rmerge, Rrim and Rpim: http://www.embl-hamburg.de/~msweiss/projects/msw_qual.html

YSBL software (space groups, Balbes-mol. replacement) http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp

Momo - to create animated diffraction image http://www.bioxray.au.dk/~bjopp/momo

Anisotropic server http://services.mbi.ucla.edu/anisoscale/

automated phasing http://www.embl-hamburg.de/Auto-Rickshaw/

mol. replacement on the all records in PDB https://portal.sbgrid.org/d/apps/wsmr/

mol. replacement: normal modes (El Nemo) and more http://www.igs.cnrs-mrs.fr/?lang=en

twin detection http://services.mbi.ucla.edu/XdVal/

space group numbers http://homepage.univie.ac.at/nikos.pinotsis/spacegroup.html

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/

Polyview-3D: make movie (figure) easily http://polyview.cchmc.org/polyview3d.html

electrostatic potential on surface - make figure http://bioserv.rpbs.univ-paris-diderot.fr/cgi-bin/PCE-Pot

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

home installation: http://bob:8099/pdb2pqr/ web input

Raster3D (open by command render (in shell); graphical output from Coot) http://skuld.bmsc.washington.edu/raster3d/

Coot manual http://www.biop.ox.ac.uk/coot/doc/coot.html#Top

SMILES (possible import of ligand to Coot): http://www.molinspiration.com/cgi-bin/properties

MONSTER: Scheme of hydrogen bonds http://monster.northwestern.edu/

Visualisation of molecules: http://personal.cscs.ch/~mvalle/ChemViz/tools.html

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

PDBCARE checks correct glycosylation http://www.glycosciences.de/tools/pdb-care/

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

ChceckMyMetal http://csgid.org/csgid/metal_sites/

protein modifications: http://dbptm.mbc.nctu.edu.tw/browse.php

generating geometrical restraints http://grade.globalphasing.org/cgi-bin/grade/server.cgi

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

Cavities and channels

Caver: http://www.caver.cz/

Hollow: surfaces and caves http://hollow.sourceforge.net/

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

Protein-protein interfaces:

Ebi-Pisa

PROTORP (protein interface) http://www.bioinformatics.sussex.ac.uk/protorp http://www.bioinformatics.sussex.ac.uk/protorp/cgi-bin/PPanalyse.pl

http://2p2idb.cnrs-mrs.fr/

5) modelling tools

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

AutoDock Vina (we have installed)

protein-protein docking: http://www.nmr.chem.uu.nl/haddock/ (necessary to install),

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/

RaptorX protein 3D structure modeling tool: http://raptorx.uchicago.edu/

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

GROMACS online https://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server

normal mode analysis http://www.sciences.univ-nantes.fr/elnemo/

6) SAXS

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

FOXS https://modbase.compbio.ucsf.edu/foxs/links.html

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) Databases

Database of lectins http://glyco3d.cermav.cnrs.fr/home.php

Mespeus database: metals in proteins http://mespeus.bch.ed.ac.uk/MESPEUS/

8) IR and Raman spectroscopy

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