Publications of the Protein Structure Bioinformatics group

2012 Ngu LH, Nijtmans LG, Distelmaier F, Venselaar H, van Emst-de Vries SE, van den Brand MA, Stoltenborg BJ, Wintjes LT, Willems PH, van den Heuvel LP, Smeitink JA, Rodenburg RJ.
A catalytic defect in mitochondrial respiratory chain complex I due to a mutation in NDUFS2 in a patient with Leigh syndrome.
Biochim Biophys Acta, Feb;1822(2):168-175. Details

2012 Doreleijers JF, Sousa da Silva AW, Krieger E, Nabuurs SB, Spronk CA, Stevens TJ, Vranken WF, Vriend G, Vuister GW.
CING: an integrated residue-based structure validation program suite.
J Biomol NMR, Nov;54(3):267-83. doi: 10.1007/s10858-012-9669-7. Details

2012 Köpfer DA, Hahn U, Ohmert I, Vriend G, Pongs O, de Groot BL, Zachariae U.
A molecular switch driving inactivation in the cardiac K+ channel HERG.
PLoS One, 7(7):e41023. Details

2012 Ajmal M, Khan MI, Micheal S, Ahmed W, Shah A, Venselaar H, Bokhari H, Azam A, Waheed NK, Collin RW, den Hollander AI, Qamar R, Cremers FP.
Identification of recurrent and novel mutations in TULP1 in Pakistani families with early-onset retinitis pigmentosa.
Mol Vis, 18:1226-1237. Details

2012 Cho HJ, Park HJ, Trexler M, Venselaar H, Lee KY, Robertson NG, Baek JI, Kang BS, Morton CC, Vriend G, Patthy L, Kim UK.
A novel COCH mutation associated with autosomal dominant nonsyndromic hearing loss disrupts the structural stability of the vWFA2 domain.
J Mol Med (Berl), Nov;90(11):1321-31. doi: 10.1007/s00109-012-0911-2. Details

2012 Harakalova M, van Harssel JJ, Terhal PA, van Lieshout S, Duran K, Renkens I, Amor DJ, Wilson LC, Kirk EP, Turner CL, Shears D, Garcia-Minaur S, Lees MM, Ross A, Venselaar H, Vriend G, Takanari H, Rook MB, van der Heyden MA, Asselbergs FW, Breur HM, Swinkels ME, Scurr IJ, Smithson SF, Knoers NV, van der Smagt JJ, Nijman IJ, Kloosterman WP, van Haelst MM, van Haaften G, Cuppen E.
Dominant missense mutations in ABCC9 cause Cantú syndrome.
Nat Genet, May 18;44(7):793-796. doi: 10.1038/ng.2324. Details

2012 Hensen U, Meyer T, Haas J, Rex R, Vriend G, Grubmüller H.
Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.
PLoS One, 7(5):e33931. Details

2012 French VM, van de Laar IM, Wessels MW, Rohe C, Roos-Hesselink JW, Wang G, Frohn-Mulder IM, Severijnen LA, de Graaf BM, Schot R, Breedveld G, Mientjes E, van Tienhoven M, Jadot E, Jiang Z, Verkerk A, Swagemakers S, Venselaar H, Rahimi Z, Najmabadi H, Meijers-Heijboer H, de Graaff E, Helbing WA, Willemsen R, Devriendt K, Belmont JW, Oostra BA, Amack JD, Bertoli-Avella AM.
NPHP4 variants are associated with pleiotropic heart malformations.
Circ Res, Jun 8;110(12):1564-1574. Details

2012 Gerrits L, Venselaar H, Wieringa B, Wansink DG, Hendriks WJ.
Phosphorylation target site specificity for AGC kinases DMPK E and Lats2.
J Cell Biochem, Jun;113(6):2126-2135. doi: 10.1002/jcb.24086. Details

2012 Peeters MC, Wisse LE, Dinaj A, Vroling B, Vriend G, Ijzerman AP.
The role of the second and third extracellular loops of the adenosine A1 receptor in activation and allosteric modulation.
Biochem Pharmacol, Jul 1;84(1):76-87. Details

2012 de Baaij JH, Stuiver M, Meij IC, Lainez S, Kopplin K, Venselaar H, Müller D, Bindels RJ, Hoenderop JG.
Membrane topology and intracellular processing of cyclin M2 (CNNM2).
J Biol Chem, Apr 20;287(17):13644-13655. Details

2012 Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, Jaravine V, Jonker HR, Kennedy MA, Lange OF, Liu G, Malliavin TE, Mani R, Mao B, Montelione GT, Nilges M, Rossi P, van der Schot G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, Vries Sd, Vuister GW, Wu B, Yang Y, Bonvin AM.
Blind testing of routine, fully automated determination of protein structures from NMR data.
Structure, Feb 8;20(2):227-236. Details

2012 Lounnas V, Vriend G.
AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.
J Chem Inf Model, Feb 27;52(2):568-576. Details

2012 Seddon G, Lounnas V, McGuire R, van den Bergh T, Bywater RP, Oliveira L, Vriend G.
Drug design for ever, from hype to hope.
J Comput Aided Mol Des, Jan;26(1):137-150. Details

2012 Krieger E, Dunbrack RL Jr, Hooft RW, Krieger B.
Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization.
Methods Mol Biol, 819:405-421. Details

2012 Gorlani A, Hulsik DL, Adams H, Vriend G, Hermans P, Verrips T.
Antibody engineering reveals the important role of J segments in the production efficiency of llama single-domain antibodies in Saccharomyces cerevisiae.
Protein Eng Des Sel, Jan;25(1):39-46. Details

2012 Doreleijers JF, Vranken WF, Schulte C, Markley JL, Ulrich EL, Vriend G, Vuister GW.
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.
Nucleic Acids Res, Jan;40(Database issue):D519-524. Details

2012 Vroling B, Thorne D, McDermott P, Joosten HJ, Attwood TK, Pettifer S, Vriend G.
NucleaRDB: information system for nuclear receptors.
Nucleic Acids Res, Jan;40(Database issue):D377-380. Details

2012 Khan M, Ajmal M, Micheal S, Azam M, Hussain A, Shahzad A, Venselaar H, Bokhari H, de Wijs I, Hoefsloot L, Waheed N, Collin R, den Hollander A, Qamar R, Cremers F.
Homozygosity mapping identifies genetic defects in four consanguineous families with retinal dystrophy from Pakistan.
Clin Genet, Nov 7. doi: 10.1111/cge.12039. [Epub ahead of print] Details

2011 van Boxtel R, Vroling B, Toonen P, Nijman IJ, van Roekel H, Verheul M, Baakman C, Guryev V, Vriend G, Cuppen E.
Systematic generation of in vivo G protein-coupled receptor mutants in the rat.
Pharmacogenomics J., Oct;11(5):326-336. Details

2011 Vroling B, Sanders M, Baakman B, Borrmann A, Verhoeven S, Klomp J, Oliveira L, De Vlieg J, Vriend G.
GPCRDB: information system for G protein-coupled receptors.
Nucleic Acids Research Advance Access published, Received September 14, 2010; Accepted October 7, 2010 Details

2011 Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.
PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
Nat Methods, Jun 29;8(7):528-529. Details

2011 Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H.
The IntAct molecular interaction database in 2010.
Nucleic Acids Res, Jan;38(Database issue):D525-531. Details

2011 Tjalsma H, Laarakkers CM, van Swelm RP, Theurl M, Theurl I, Kemna EH, van der Burgt YE, Venselaar H, Dutilh BE, Russel FG, Weiss G, Masereeuw R, Fleming RE, Swinkels DW.
Mass Spectrometry Analysis of Hepcidin Peptides in Experimental Mouse Models.
PLoS ONE , Mar 8;6(3):e16762. Details

2011 van de Laar IM, Oldenburg RA, Pals G, Roos-Hesselink JW, de Graaf BM, Verhagen JM, Hoedemaekers YM, Willemsen R, Severijnen LA, Venselaar H, Vriend G, Pattynama PM, Collée M, Majoor-Krakauer D, Poldermans D, Frohn-Mulder IM, Micha D, Timmermans J, Hilhorst-Hofstee Y, Bierma-Zeinstra SM, Willems PJ, Kros JM, Oei EH, Oostra BA, Wessels MW, Bertoli-Avella AM.
Mutations in SMAD3 cause a syndromic form of aortic aneurysms and dissections with early-onset osteoarthritis.
Nat Genet, Feb;43(2):121-126. Details

2011 Eijsink VG, Matthews BW, Vriend G.
The role of calcium ions in the stability and instability of a thermolysin-like protease.
Protein Sci, 20(8):1346-1355. Details

2011 Touw WG, Vriend G.
On the complexity of Engh and Huber refinement restraints: the angle τ as example.
Acta Crystallogr D Biol Crystallogr, Dec;66(Pt 12):1341-1350. Details

2011 Joosten RP, te Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C, Vriend G.
A series of PDB related databases for everyday needs.
Nucleic Acids Res, Jan;39(Database issue):D411–D419. Details

2011 Poulton CJ, Schot R, Kia SK, Jones M, Verheijen FW, Venselaar H, de Wit MC, de Graaff E, Bertoli-Avella AM, Mancini GM.
Microcephaly with simplified gyration, epilepsy, and infantile diabetes linked to inappropriate apoptosis of neural progenitors.
Am J Hum Genet, Aug 12;89(2):265-276. Details

2011 Vissers LE, Lausch E, Unger S, Campos-Xavier AB, Gilissen C, Rossi A, Del Rosario M, Venselaar H, Knoll U, Nampoothiri S, Nair M, Spranger J, Brunner HG, Bonafé L, Veltman JA, Zabel B, Superti-Furga A.
Chondrodysplasia and abnormal joint development associated with mutations in IMPAD1, encoding the Golgi-resident nucleotide phosphatase, gPAPP.
Am J Hum Genet, May 13;88(5):608-615. Details

2011 Camilli F, Borrmann A, Gholizadeh S, te Beek TA, Kuipers R, Venselaar H.
The future of HOPE: what can and cannot be predicted about the molecular effects of a disease causing point mutation in a protein?
EMBnet.journal , 17(1):25-37. Details

2011 Breukels V, Konijnenberg A, Nabuurs SM, Doreleijers JF, Kovalevskaya NV, Vuister GW.
Overview on the use of NMR to examine protein structure.
Curr Protoc Protein Sci, Apr;Chapter 17:Unit17.5. Details

2011 Snelders E, Karawajczyk A, Verhoeven RJ, Venselaar H, Schaftenaar G, Verweij PE, Melchers WJ.
The structure-function relationship of the Aspergillus fumigatuscyp51A L98H conversion by site-directed mutagenesis: The mechanism of L98H azole resistance.
Fungal Genet Biol, Nov;48(11):1062-7100. Details

2011 Cerdobbel A, De Winter K, Aerts D, Kuipers R, Joosten HJ, Soetaert W, Desmet T.
Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis.
Protein Eng Des Sel, Nov;24(11):829-834. Details

2011 Roumen L, Sanders MP ,Vroling B, de Esch IJ, de Vlieg J, Leurs R, Klomp JP, Nabuurs SB, de Graaf C.
In Silico Veritas: The Pitfalls and Challenges of Predicting GPCR-Ligand Interactions.
Pharmaceuticals, 4(9):1196-1215. Details

2011 Vroling B, Thorne D, McDermott P, Attwood TK, Vriend G, Pettifer S.
Integrating GPCR-specific information with full text articles.
BMC Bioinformatics, 12:362 Details

2011 Sanders MP, Verhoeven S, de Graaf C, Roumen L, Vroling B, Nabuurs SB, de Vlieg J, Klomp JP.
Snooker: A Structure-Based Pharmacophore Generation Tool Applied to Class A GPCRs.
J Chem Inf Model, Sep 26;51(9):2277-2292. Details

2011 Kufareva I, Rueda M, Katritch V, GPCR Dock 2010 participants, Stevens RC, Abagyan R.
Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment.
Structure, Aug 10;19(8):1108-1126. Details

2011 Smits P, Antonicka H, van Hasselt PM, Weraarpachai W, Haller W, Schreurs M, Venselaar H, Rodenburg RJ, Smeitink JA, van den Heuvel LP.
Mutation in subdomain G' of mitochondrial elongation factor G1 is associated with combined OXPHOS deficiency in fibroblasts but not in muscle.
Eur J Hum Genet, Mar;19(3):275-279. Details

2011 Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C.
BioinformaticsTraining Network (BTN): a community resource for bioinformatics trainers.
Brief Bioinform, doi: 10.1093/bib/bbr064. Details

2011 Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A.
Automatic rebuilding and optimization of crystallographic structures in the PDB.
Bioinformatics, Dec 15;27(24):3392-3398. Details

2011 Weegerink NJ, Schraders M, Oostrik J, Huygen PL, Strom TM, Granneman S, Pennings RJ, Venselaar H, Hoefsloot LH, Elting M, Cremers CW, Admiraal RJ, Kremer H, Kunst HP.
Genotype-phenotype correlation in DFNB8/10 families with TMPRSS3 mutations.
J Assoc Res Otolaryngol, Dec;12(6):753-766. Details

2011 Doreleijers JF, Vranken WF, Schulte C, Markley JL, Ulrich EL, Vriend G, Vuister GW.
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.
Nucleic Acids Res, Jan;40(Database issue):D519-524. Details

2011 Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH.
A new generation of crystallographic validation tools for the protein data bank.
Structure, Oct 12;19(10):1395-1412. Details

2011 Rosentul DC, Plantinga TS, Papadopoulos A, Joosten LA, Antoniadou A, Venselaar H, Kullberg BJ, van der Meer JW, Giamarellos-Bourboulis EJ, Netea MG.
Variation in genes of β-glucan recognition pathway and susceptibility to opportunistic infections in HIV-positive patients.
Immunol Invest, 40(7-8):735-750. Details

2010 van der Wijst J, Glaudemans B, Venselaar H, Nair AV, Forst AL, Hoenderop JG, Bindels RJ.
Functional analysis of the Kv1.1 N255D mutation associated with autosomal dominant hypomagnesemia.
J Biol Chem, Jan 1;285(1):171-178. Details

2010 Schuemie MJ, Kang N, Hekkelman ML, Kors JA.
GeneE: gene and protein query expansion with disambiguation.
Bioinformatics, Jan 1;26(1):147-148. Details

2010 van der Velden LM, Stapelbroek JM, Krieger E, van den Berghe PV, Berger R, Verhulst PM, Holthuis JC, Houwen RH, Klomp LW, van de Graaf SF.
Folding defects in P-type ATP 8B1 associated with hereditary cholestasis are ameliorated by 4-phenylbutyrate.
Hepatology, Jan;51(1):286-296. Details

2010 Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM, Partners I, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G, Vriend G.
The EMBRACE web service collection.
Nucleic Acids Res, 38(Web Server issue):W683-688. Details

2010 Hekkelman ML, Te Beek TA, Pettifer SR, Thorne D, Attwood TK, Vriend G.
WIWS: a protein structure bioinformatics Web service collection.
Nucleic Acids Res, Jul 1;38 Suppl:W719-723. Details

2010 Khelashvili G, Dorff K, Shan J, Camacho-Artacho M, Skrabanek L, Vroling B, Bouvier M, Devi LA, George SR, Javitch JA, Lohse MJ, Milligan G, Neubig RR, Palczewski K, Parmentier M, Pin JP, Vriend G, Campagne F, Filizola M.
GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.
Bioinformatics, Jul 15;26(14):1804-1805. Details

2010 Kuipers RK, Joosten HJ, van Berkel WJ, Leferink NG, Rooijen E, Ittmann E, van Zimmeren F, Jochens H, Bornscheuer U, Vriend G, dos Santos VA, Schaap PJ.
3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities.
Proteins, Jul;78(9):2101-2113. Details

2010 Huberts DH, Venselaar H, Vriend G, Veenhuis M, der Klei IJ.
The moonlighting function of pyruvate carboxylase resides in the non-catalytic end of the TIM barrel.
Biochim Biophys Acta, Sep;1803(9):1038-1042. Details

2010 Sun Y, Almomani R, Aten E, Celli J, van der Heijden J, Venselaar H, Robertson SP, Baroncini A, Franco B, Basel-Vanagaite L, Horii E, Drut R, Ariyurek Y, den Dunnen JT, Breuning MH.
Terminal Osseous Dysplasia Is Caused by a Single Recurrent Mutation in the FLNA Gene.
Am J Hum Genet, Jul 9;87(1):146-153. Details

2010 Nikopoulos K, Venselaar H, Collin RW, Riveiro-Alvarez R, Boonstra FN, Hooymans JM, Mukhopadhyay A, Shears D, van Bers M, de Wijs IJ, van Essen AJ, Sijmons RH, Tilanus MA, van Nouhuys CE, Ayuso C, Hoefsloot LH, Cremers FP.
Overview of the mutation spectrum in familial exudative vitreoretinopathy and Norrie disease with identification of 21 novel variants in FZD4, LRP5, and NDP.
Hum Mutat, Jun;31(6):656-666. Details

2010 Waanders E, Venselaar H, te Morsche RH, de Koning DB, Kamath PS, Torres VE, Somlo S, Drenth JP.
Secondary and tertiary structure modeling reveals effects of novel mutations in polycystic liver disease genes PRKCSH and SEC63.
Clin Genet, Jul;78(1):47-56. Details

2010 Venselaar H, Joosten RP, Vroling B, Baakman CA, Hekkelman ML, Krieger E, Vriend G.
Homology modelling and spectroscopy, a never-ending love story.
Eur Biophys J, Mar;39(4):551-563. Details

2010 Dölker N, Zachariae U, Grubmüller H.
Hydrophilic linkers and polar contacts affect aggregation of FG repeat peptides.
Biophys J, Jun 2;98(11):2653-2661. Details

2010 Stary A, Wacker SJ, Boukharta L, Zachariae U, Karimi-Nejad Y, Aqvist J, Vriend G, de Groot BL.
Toward a consensus model of the HERG potassium channel.
ChemMedChem, Mar 1;5(3):455-467. Details

2010 Middelbeek J, Clark K, Venselaar H, Huynen MA, van Leeuwen FN.
The alpha-kinase family: an exceptional branch on the protein kinase tree.
Cellulair and molecular life sciences, 67(6):875-890. Details

2010 Kourist R, Jochens H, Bartsch S, Kuipers R, Padhi SK, Gall M, Böttcher D, Joosten HJ, Bornscheuer UT.
The α/β-Hydrolase Fold 3DM Database (ABHDB) as a Tool for Protein
ChemBioChem, 11:1635–1643. Details

2010 Kuipers R, van den Bergh T, Joosten HJ, Lekanne Dit Deprez RH, Mannens MM, Schaap PJ.
Novel tools for extraction and validation of disease-related mutations applied to fabry disease.
Hum Mutat, Sep;31(9):1026-1032. Details

2009 Thornton J, Vriend G.
Annotations for all by all - the BioSapiens network.
Genome Biology, 10:401. Details

2009 Kleefstra T, van Zelst-Stams WA, Nillesen WM, Cormier-Daire V, Houge G, Foulds N, van Dooren M, Willemsen MH, Pfundt R, Turner A, Wilson M, McGaughran J, Rauch A, Zenker M, Adam M, Innes M, Davies C, González-Meneses López A, Casalone R, Weber A, Brueton LA, Delicado Navarro A, Palomares Bralo M, Venselaar H, Stegmann SP, Yntema HG, van Bokhoven H, Brunner HG.
Further clinical and molecular delineation of the 9q Subtelomeric Deletion Syndrome supports a major contribution of EHMT1 haploinsufficiency to the core phenotype.
J Med Genet, Sep;46(9):598-606. Details

2009 van der Woning SP, Venselaar H, van Rotterdam W, Jacobs-Oomen S, van Leeuwen JE, van Zoelen EJ.
Role of the C-terminal linear region of EGF-like growth factors in ErbB specificity.
Growth Factors, Jun;27(3):163-172. Details

2009 Joosten RP, Womack T, Vriend G, Bricogne G.
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.
Acta Crystallogr D Biol Crystallogr, Feb;65(Pt 2):176-185. Details

2009 Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund A, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K,Pagni M, Reichstadt M,Breton V, Tickle IJ, Vriend G.
PDB_REDO: automated re-refinement of X-ray structure models in the PDB.
J. Appl. Cryst, 42:376-384. Details

2009 Kuipers RK, Joosten HJ, Verwiel E, Paans S, Akerboom J, van der Oost J, Leferink NG, van Berkel WJ, Vriend G, Schaap PJ.
Correlated mutation analyses on super-family alignments reveal functionally important residues.
Proteins, Aug 15;76(3):608-616. Details

2009 Narayanan B, Niu W, Joosten HJ, Li Z, Kuipers RK, Schaap PJ, Dunaway-Mariano D, Herzberg O.
Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member.
J Mol Biol, Feb 20;386(2):486-503. Details

2009 Pettifer S, Thorne D, McDermott P, Attwood T, Baran J, Bryne JC, Hupponen T, Mowbray D, Vriend G.
An active registry for bioinformatics web services.
Bioinformatics, Aug 15;25(16):2090-2091. Details

2009 Sanderson K.
New protein structures replace the old. Dutch software to weed out errors in Protein Data Bank.
Nature News, 459:1038-1039. Details

2009 Doreleijers JF, Vranken WF, Schulte C, Lin J, Wedell JR, Penkett CJ, Vuister GW, Vriend G, Markley JL, Ulrich EL.
The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries.
J Biomol NMR, Dec;45(4):389-396. Details

2009 Lee HK, Song MH, Kang M, Lee JT, Kong KA, Choi SJ, Lee KY, Venselaar H, Vriend G, Lee WS, Park HJ, Kwon TK, Bok J, Kim UK.
Clinical and molecular characterizations of novel POU3F4 mutations reveal that DFN3 is due to null function of POU3F4 protein.
Physiol Genomics, Nov 6;39(3):195-201. Details

2009 Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K.
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.
Proteins, 12;77(S9):114-122. Details

2009 Bagaria A, Baker D, Bardiaux B, Bonvin AM, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker H, Mao B, Malliavin TE, Montelione GT, Nilges M, Raman S, Rosato A, Schot Gvd, Vranken WF, Vuister GW.
CASD-NMR: critical assessment of automated structure determination by NMR.
Nat Methods, Sep;6(9):625-626. Details

2009 Ferwerda B, Ferwerda G, Plantinga TS, Willment JA, van Spriel AB, Venselaar H, Elbers CC, Johnson MD, Cambi A, Huysamen C, Jacobs L, Jansen T, Verheijen K, Masthoff L, Morré SA, Vriend G, Williams DL, Perfect JR, Joosten LA, Wijmenga C, van der Meer JW, Adema GJ, Kullberg BJ, Brown GD, Netea MG.
Human dectin-1 deficiency and mucocutaneous fungal infections.
N Engl J Med, Oct 29;361(18):1760-1767. Details

2009 Littink KW, van Genderen MM, Collin RW, Roosing S, de Brouwer AP, Riemslag FC, Venselaar H, Thiadens AA, Hoyng CB, Rohrschneider K, den Hollander AI, Cremers FP, van den Born LI.
A novel homozygous nonsense mutation in CABP4 causes congenital cone-rod synaptic disorder.
Invest Ophthalmol Vis Sci, May;50(5):2344-2350. Details

2009 van den Berghe PV, Stapelbroek JM, Krieger E, de Bie P, van de Graaf SF, de Groot RE, van Beurden E, Spijker E, Houwen RH, Berger R, Klomp LW.
Reduced expression of ATP7B affected by Wilson disease-causing mutations is rescued by pharmacological folding chaperones 4-phenylbutyrate and curcumin.
Hepatology, Dec;50(6):1783-1795. Details

2009 Zachariae U, Giordanetto F, Leach AG.
Side chain flexibilities in the human ether-a-go-go related gene potassium channel (hERG) together with matched-pair binding studies suggest a new binding mode for channel blockers.
J Med Chem, Jul 23;52(14):4266-4276. Details

2009 Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker HR, Mao B, Malliavin TE, Montelione GT, Nilges M, Raman S, van der Schot G, Vranken WF, Vuister GW, Bonvin AM.
CASD-NMR: critical assessment of automated structure determination by NMR.
Nat Methods, Sep;6(9):625-626. Details

2008 Zachariae U, Schneider R, Velisetty P, Lange A, Seeliger D, Wacker SJ, Karimi-Nejad Y, Vriend G, Becker S, Pongs O, Baldus M, de Groot BL.
The molecular mechanism of toxin-induced conformational changes in a potassium channel: Relation to C-type inactivation.
Structure, May 7;16(5):747-754. Details

2008 Collin RWJ, Chellappa R, Pauw RJ, Vriend G, Oostrik J, van Drunen W, Huygen PL, Admiraal R, Hoefsloot LH, Cremers FP, Xiang M, Cremers CW, Kremer H.
Missense mutations in POU4F3 cause autosomal dominant hearing impairment DFNA15 and affect subcellular localization and DNA binding.
Human Mutation, Apr;29(4):545-554. Details

2008 Ye K, Vriend G, IJzerman AP.
Tracing evolutionary pressure.
Bioinformatics, Apr 1;24(7):908-15. Details

2008 Collin RWJ, Kalay E, Tariq M, Peters T, van der Zwaag B, Venselaar H, Oostrik J, Lee K, Ahmed ZM, Caylan R, Li Y, Spierenburg HA, Eyupoglu E, Heister A, Riazuddin S, Bahat E, Ansar M, Arslan S, Wollnik B, Brunner HG, Cremers CW, Karaguzel A, Ahmad W, Cremers FP, Vriend G, Friedman TB, Riazuddin S, Leal SM, Kremer H.
Mutations of ESRRB encoding estrogen-related receptor beta cause autosomal-recessive nonsyndromic hearing impairment DFNB35.
American Journal of Human Genetics, Jan;82(1):125-138. Details

2008 von Grotthuss M, Plewczynski D, Vriend G, Rychlewski L.
3D-Fun: predicting enzyme function from structure.
Nucleic Acids Res, Jul 1;36(Web Server issue):W303-307. Details

2008 Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL.
BioMagResBank.
Nucleic Acids Res , 36(Database issue):D402-408. Details

2008 Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM.
Remediation of the protein data bank archive.
Nucleic Acids Res , 36(Database issue):D426-433. Details

2008 Lütteke, T.
Web Resources for the Glycoscientist.
Chembiochem, Sep 1;9(13):2155-2160. Details

2008 El-Sheikh AA, van den Heuvel JJ, Krieger E, Russel FG, Koenderink JB.
Functional Role of Arginine 375 in Transmembrane Helix 6 of Multidrug Resistance Protein 4 (MRP4/ABCC4).
Mol Pharmacol, Oct;74(4):964-971. Details

2008 Ahmed ZN, Masmoudi S, Kalay E, Belyantseva IA, Mosrati MA, Collin RWJ, Riazuddin S, Hmani-Aifa E, Venselaar H, Kawar MN, Tlili A, Van der Zwaag B, Khan SY, Ayadi L, Riazuddin SA, Morell RJ, Griffith AJ, Charfedine I, Çaylan R, Oostrik J, Karaguzel A, Ghorbel A ,Riazuddin S, Friedman TB, Ayadi H, Kremer H.
Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans.
Nature Genetics, 40:1335-1340 Details

2008 Ahmed ZM,Riazuddin S, Aye S, Ali RA, Venselaar H, Anwar S, Belyantseva PP, Qasim M, Riazuddin S , Friedman TB.
Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.
Hum Genet, Oct;124(3):215-223. Details

2008 Thébault S, Cao G, Venselaar H, Xi Q, Bindels RJM, Hoenderop JGJ.
Role of the alpha-kinase domain in TRPM6 channel and regulation by intracellular ATP.
J Biol Chem, Jul 18;283(29):19999-20007. Details

2008 Swinkels DW, Venselaar H, Wiegerinck ET, Bakker E, Joosten I, Jaspers CAJJ, Vasmel WL, Breuning MA.
A novel (Leu183Pro-)mutation in the HFE-gene co-inherited with the Cys282Tyr mutation in two unrelated Dutch hemochromatosis patients.
Blood Cells Mol Dis, May-Jun;40(3):334-338. Details

2008 Narayanan B, Niu W, Joosten HJ, Li Z, Kuipers RK, Schaap PJ, Dunaway-Mariano D, Herzberg O.
Structure and Function of 2,3-Dimethylmalate Lyase, a PEP Mutase/Isocitrate Lyase Superfamily Member.
J Mol Biol, Feb 20;386(2):486-503. Details

2008 Littink KW, van Genderen MM, Collin RW, Roosing S, de Brouwer AP, Riemslag FC, Venselaar H, Thiadens AA, Hoyng CB, Rohrschneider K, den Hollander AI, Cremers FP, van den Born LI.
A novel homozygous nonsense mutation in CABP4 causes congenital cone-rod synaptic disorder.
Invest Ophthalmol Vis Sci, May;50(5):2344-2350. Details

2007 Kalay E, Uzumcu A, Krieger E, Caylan R, Uyguner O, Ulubil-Emiroglu M, Erdol H, Kayserili H, Hafiz G, Baerer N, Heister AJ, Hennies HC, Nurnberg P, Baaran S, Brunner HG, Cremers CW, Karaguzel A, Wollnik B, Kremer H.
MYO15A (DFNB3) mutations in Turkish hearing loss families and functional modeling of a novel motor domain mutation.
Am J Med Genet A, 143(20):2382-2389. Details

2007 Gosens I, van Wijk E, Kersten FF, Krieger E, van der Zwaag B, Marker T, Letteboer SJ, Dusseljee S, Peters T, Spierenburg HA, Punte IM, Wolfrum U, Cremers FP, Kremer H, Roepman R.
MPP1 links the Usher protein network and the Crumbs protein complex in the retina.
Hum Mol Genet, 16(16):1993-2003. Details

2007 Joosten RP, Vriend G.
PDB improvement starts with data deposition.
Science, 317(5835):195-196. Details

2007 Skrabanek L, Murcia M, Bouvier M, Devi L, George SR, Lohse MJ, Milligan G, Neubig R, Palczewski K, Parmentier M, Pin JP, Vriend G, Javitch JA, Campagne F, Filizola M.
Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base.
BMC Bioinformatics, 8:177. Details

2007 Meijer JT, Roeters M, Viola V, Löwik DW, Vriend G, van Hest JC.
Stabilization of peptide fibrils by hydrophobic interaction.
Langmuir, 23(4):2058-2063. Details

2007 Folkertsma S, van Noort PI, de Heer A, Carati P, Brandt R, Visser A, Vriend G, de Vlieg J.
The use of in vitro peptide binding profiles and in silico ligand-receptor interaction profiles to describe ligand-induced conformations of the retinoid X receptor alpha ligand-binding domain.
Mol Endocrinol, Jan;21(1):30-48. Details

2007 Oti M, Brunner HG.
The modular nature of genetic diseases.
Clin Genet, Jan;71(1):1-11. Details

2007 Maillard J, Spronk CA, Buchanan G, Lyall V, Richardson DJ, Palmer T, Vuister GW, Sargent F.
Structural diversity in twin-arginine signal peptide-binding proteins.
Proc Natl Acad Sci U S A, Oct 2;104(40):15641-15646. Details

2006 van Driel MA, Bruggeman J, Vriend G, Brunner HG, Leunissen JA.
A text-mining analysis of the human phenome.
Eur J Hum Genet, May;14(5):535-542. Details

2006 Harjes E, Harjes S, Wohlgemuth S, Muller KH , Krieger E, Herrmann C, Bayer P.
GTP-Ras Disrupts the Intramolecular Complex of C1 and RA Domains of Nore1.
Structure, May;14(5):881-888. Details

2006 Krieger E, Nielsen JE, Spronk CA, Vriend G.
Fast empirical pK(a) prediction by Ewald summation.
J Mol Graph Model, Dec;25(4):481-486. Details

2006 Lugtenberg D, Yntema HG, Banning MJ, Oudakker AR, Firth HV, Willatt L, Raynaud M, Kleefstra T, Fryns JP, Ropers HH, Chelly J, Moraine C, Gecz J, Reeuwijk J, Nabuurs SB, de Vries BB, Hamel BC, de Brouwer AP, Bokhoven H.
ZNF674: A New Kruppel-Associated Box-Containing Zinc-Finger Gene Involved in Nonsyndromic X-Linked Mental Retardation.
Am J Hum Genet, Feb;78(2):265-278. Details

2006 Moita LF, Vriend G, Mahairaki V, Louis C, Kafatos FC.
Integrins of Anopheles gambiae and a putative role of a new beta integrin, BINT2, in phagocytosis of E-coli.
Insect Biochem Mol Biol, Apr;36(4):282-290. Details

2006 Nabuurs SB, Spronk CA, Vuister GW, Vriend G.
Traditional biomolecular structure determination by NMR spectroscopy allows for major errors.
PLoS Comput Biol, Feb;2(2):e9. Details

2006 Van Durme J, Horn F, Costagliola S, Vriend G, Vassart G.
GRIS: Glycoprotein-hormone Receptor Information System.
Mol Endocrinol, Sep;20(9):2247-2255. Details

2006 Ott MA, Vriend G.
Correcting ligands, metabolites, and pathways.
BMC Bioinformatics, Nov 28;7:517. Details

2006 van der Woning SP, van Rotterdam W, Nabuurs SB, Venselaar H, Jacobs-Oomen S, Wingens M, Vriend G, Stortelers C, van Zoelen EJ.
Negative constraints underlie the ErbB specificity of epidermal growth factor-like ligands.
Journal of Biological Chemistry, Dec 29;281(52):40033-40040. Details

2006 Paiva AC, Oliveira L, Horn F, Bywater RP, Vriend G.
Modeling GPCRs.
Ernst Schering Found Symp Proc, (2):23-47 Details

2006 Horn SJ, Sikorski P, Cederkvist JB, Vaaje-Kolstad G, Sørlie M, Synstad B, Vriend G, Vårum KM, Eijsink VG.
Costs and benefits of processivity in enzymatic degradation of recalcitrant polysaccharides.
Proc Natl Acad Sci U S A, Nov 28;103(48):18089-18094. Details

2006 Smeitink JA, Elpeleg O, Antonicka H, Diepstra H, Saada A, Smits P, Sasarman F, Vriend G, Jacob-Hirsch J, Shaag A, Rechavi G, Welling B, Horst J, Rodenburg RJ, van den Heuvel B, Shoubridge EA.
Distinct clinical phenotypes associated with a mutation in the mitochondrial translation elongation factor EFTs.
Am J Hum Genet, Nov;79(5):869-877. Details

2006 Smith BJ, Huyton T, Joosten RP, McKimm-Breschkin JL, Zhang JG, Luo CS, Lou MZ, Labrou NE, Garrett TP.
Structure of a calcium-deficient form of influenza virus neuraminidase: implications for substrate binding.
Acta Crystallogr D Biol Crystallogr, Sep;62(Pt 9):947-952. Details

2005 Dolk E, van der Vaart M, Lutje Hulsik D, Vriend G, de Haard H, Spinelli S, Cambillau C, Frenken L, Verrips T.
Isolation of llama antibody fragments for prevention of dandruff by phage display in shampoo.
Appl Environ Microbiol, Jan;71(1):442-450. Details

2005 Dolk E, van Vliet C, Perez JM, Vriend G, Darbon H, Ferrat G, Cambillau C, Frenken LG, Verrips T.
Induced refolding of a temperature denatured llama heavy-chain antibody fragment by its antigen.
Proteins, May 15;59(3):555-564. Details

2005 van Driel MA, Cuelenaere K, Kemmeren PP, Leunissen JA, Brunner HG, Vriend G.
GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases.
Nucleic Acids Res, Jul 1;33(Web Server issue):W758-761. Details

2005 Duquesne AE, Ruijter M, Brouwer J, Drijfhout JW, Nabuurs SB, Spronk CA, Vuister GW, Ubbink M, Canters GW.
Solution structure of the second PDZ domain of the neuronal adaptor X11alpha and its interaction with the C-terminal peptide of the human copper chaperone for superoxide dismutase.
J Biomol NMR, Jul;32(3):209-218. Details

2005 Hekkelman ML, Vriend G.
MRS: a fast and compact retrieval system for biological data.
Nucleic Acids Res, Jul 1;33(Web Server issue):W766-9. Details

2005 Kalay E, de Brouwer AP, Caylan R, Nabuurs SB, Wollnik B, Karaguzel A, Heister JG, Erdol H, Cremers FP, Cremers CW, Brunner HG, Kremer H.
A novel D458V mutation in the SANS PDZ binding motif causes atypical Usher syndrome.
J Mol Med, Dec;83(12):1025-1032. Details

2005 Kantardzhieva A, Gosens I, Alexeeva S, Punte IM, Versteeg I, Krieger E, Neefjes-Mol CA, den Hollander AI, Letteboer SJ, Klooster J, Cremers FP, Roepman R, Wijnholds J.
MPP5 recruits MPP4 to the CRB1 complex in photoreceptors.
Invest Ophthalmol Vis Sci, Jun;46(6):2192-2201. Details

2005 Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CA, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AM.
RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank.
Proteins, Jun 1;59(4):662-672. Details

2005 Nabuurs SB, Krieger E, Spronk CA, Nederveen AJ, Vriend G, Vuister GW.
Definition of a new information-based per-residue quality parameter.
J Biomol NMR, Oct;33(2):123-134. Details

2005 de Pont J, Qui LY, Krieger E, Schaftenaar G, Swarts HGP, Willems P, Koenderink JB.
Elucidation of the ouabain-binding site in Na-KATPase by chimeric approaches.
Journal of General Physiology, 126(1):9-10.

2005 Qiu LY, Krieger E, Schaftenaar G, Swarts HG, Willems PH, De Pont JJ, Koenderink JB.
Reconstruction of the complete ouabain-binding pocket of Na,K-ATPase in gastric H,K-ATPase by substitution of only seven amino acids.
Journal of Biological Chemistry, Sep 16;280(37):32349-32355. Details

2005 Swarts HG, Koenderink JB, Willems PH, Krieger E, De Pont JJ.
Asn792 participates in the hydrogen bond network around the K+-binding pocket of gastric H,K-ATPase.
J Biol Chem, Mar 25;280(12):11488-11494. Details

2004 Brunner HG, van Driel MA.
From syndrome families to functional genomics.
Nature Reviews Genetics , Jul;5(7):545-551. Details

2004 Eijsink VG, Bjork A, Gaseidnes S, Sirevag R, Synstad B, van den Burg B, Vriend G.
Rational engineering of enzyme stability.
J Biotechnol, Sep 30;113(1-3):105-120. Details

2004 Folkertsma S, van Noort P, Van Durme J, Joosten HJ, Bettler E, Fleuren W, Oliveira L, Horn F, de Vlieg J, Vriend G.
A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain.
J Mol Biol, Aug 6;341(2):321-335. Details

2004 Koenderink JB, Swarts HG, Willems PH, Krieger E, De Pont JJ.
A conformation-specific interhelical salt bridge in the K+ binding site of gastric H,K-ATPase.
J Biol Chem, Apr 16;279(16):16417-16424. Details

2004 Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G.
Making optimal use of empirical energy functions: Force-field parameterization in crystal space.
Proteins, Dec 1;57(4):678-683. Details

2004 Krieger E, Geretti E, Brandner B, Goger B, Wells TN, Kungl AJ.
A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations.
Proteins, Mar 1;54(4):768-775. Details

2004 Le Guezennec X, Vriend G, Stunnenberg HG.
Molecular determinants of the interaction of Mad with the PAH2 domain of mSin3.
J Biol Chem, Jun 11;279(24):25823-25829. Details

2004 Luijendijk MW, Van Wijk E, Bischoff AM, Krieger E, Huygen PL, Pennings RJ, Brunner HG, Cremers CW, Cremers FP, Kremer H.
Identification and molecular modelling of a mutation in the motor head domain of myosin VIIA in a family with autosomal dominant hearing impairment.
Hum Genet, Jul;115(2):149-156. Details

2004 Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF,Bonvin AMJJ, Vuister GW, Vriend G, Spronk CAEM.
DRESS: a Database of REfined Solution NMR Structures.
Proteins, May 15;55(3):483-486. Details

2004 Nabuurs SB, Spronk CAEM, Vriend G, Vuister GW.
Concepts and tools for NMR restraint analysis and validation.
Concepts in Magnetic Resonance, 22A(2):90-105. Details

2004 Oliveira L, Hulsen T, Lutje Hulsik D, Paiva AC, Vriend G.
Heavier-than-air flying machines are impossible.
FEBS Lett, Apr 30;564(3):269-273. Details

2004 Spronk CA, Nabuurs SB, Krieger E, Vriend G, Vuister GW.
Validation of protein structures derived by NMR spectroscopy.
Progress in NMR spectroscopy, 45:315-337. Details

2004 Synstad B, Gaseidnes S, Van Aalten DM, Vriend G, Nielsen JE, Eijsink VG.
Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase.
Eur J Biochem, Jan;271(2):253-262. Details

2004 Vriend G.
Protein design: quo vadis?
Science, Nov 12;306(5699):1135. Details

2004 Walma T, Aelen J, Nabuurs SB, Oostendorp M, van den Berk L, Hendriks W, Vuister GW.
A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL.
Structure , Jan;12(1):11-20. Details

2003 Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G.
GPCRDB information system for G protein-coupled receptors.
Nucleic Acids Res, Jan 1;31(1):294-297. Details

2003 Bettler E, Krause R, Horn F, Vriend G.
NRSAS: Nuclear Receptor Structure Analysis Servers.
Nucleic Acids Res, Jul 1;31(13):3400-3403. Details

2003 Campagne F, Bettler E, Vriend G, Weinstein H.
Batch mode generation of residue-based diagrams of proteins.
Bioinformatics , Sep 22;19(14):1854-1855. Details

2003 Go SL, Maugeri A, Mulder JJ, van Driel MA, Cremers FP, Hoyng CB.
Autosomal Dominant Rhegmatogenous Retinal Detachment Associated with an Arg453Ter Mutation in the COL2A1 Gene.
Invest Ophthalmol Vis Sci, Sep;44(9):4035-4043. Details

2003 van den Hurk JA, van de Pol DJ, Wissinger B, van Driel MA, Hoefsloot LH, de Wijs IJ, van den Born LI, Heckenlively JR, Brunner HG, Zrenner E, Ropers HH, Cremers FP.
Novel types of mutation in the choroideremia(CHM) gene: a full-length L1 insertion and an intronic mutation activating a cryptic exon.
Hum Genet, Aug;113(3):268-275. Details

2003 van Driel MA, Cuelenaere K, Kemmeren PPCW, Leunissen JAM, Brunner HG .
A new web-based data mining tool for the identification of candidate genes for human genetic disorders.
Eur. J. Human Genet, Jan;11(1):57-63. Details

2003 Van Durme JJ, Bettler E, Folkertsma S, Horn F, Vriend G.
NRMD: Nuclear Receptor Mutation Database.
Nucleic Acids Res, Jan 1;31(1):331-333. Details

2003 Krieger E, Nabuurs SB, Vriend G.
Homology Modeling.
Methods Biochem. Anal, 44:509-523. Details

2003 van Wijk E, Krieger E, Kemperman MH, De Leenheer EM, Huygen PL, Cremers CW, Cremers FP, Kremer H.
A mutation in the gamma actin 1 (ACTG1) gene causes autosomal dominant hearing loss (DFNA20/26).
J Med Genet, Dec;40(12):879-884. Details

2003 Boteva R, Koek A, Visser NV, Visser AJ, Krieger E, Zlateva T, Veenhuis M, van der Klei I.
Fluorescence analysis of the Hansenula polymorpha peroxisomal targeting signal-1 receptor, Pex5p.
Eur J Biochem, Nov;270(21):4332-4338. Details

2003 Bonifati V, Rizzu P, Squitieri F, Krieger E, Vanacore N, van Swieten JC, Brice A, van Duijn CM, Oostra B, Meco G, Heutink P.
DJ-1( PARK7), a novel gene for autosomal recessive, early onset parkinsonism.
Neurol Sci, Oct;24(3):159-160. Details

2003 van Swieten JC, Brusse E, de Graaf BM, Krieger E, van de Graaf R, de Koning I, Maat-Kievit A, Leegwater P, Dooijes D, Oostra BA, Heutink P.
A mutation in the fibroblast growth factor 14 gene is associated with autosomal dominant cerebellar ataxia.
Am J Hum Genet, Apr;72(4):1078. Details

2003 Bonifati V, Rizzu P, van Baren MJ, Schaap O, Breedveld GJ, Krieger E, Dekker MC, Squitieri F, Ibanez P, Joosse M, van Dongen JW, Vanacore N, van Swieten JC,Brice A, Meco G, van Duijn CM, Oostra BA, Heutink P.
Mutations in the DJ-1 gene associated with autosomal recessive early-onset parkinsonism.
Science, Jan 10;299(5604):256-259. Details

2003 Nabuurs SB, Krieger E, Spronk CAEM, Hooft RWW, Vriend G.
Protein Structures: What good is beauty if it cannot be seen?
Computational Medicinal Chemistry and Drug Discovery, Marcel Dekker Inc:387-402.

2003 Nabuurs SB, Spronk CA, Krieger E, Maassen H, Vriend G, Vuister GW.
Quantitative evaluation of experimental NMR restraints.
J Am Chem Soc, Oct 1;125(39):12026-12034. Details

2003 de Brouwer AP, Pennings RJ, Roeters M, Van Hauwe P, Astuto LM, Hoefsloot LH, Huygen PL, van den Helm B, Deutman AF, Bork JM, Kimberling WJ, Cremers FP, Cremers CW, Kremer H.
Mutations in the calcium-binding motifs of CDH23 and the 35delG mutation in GJB2 cause hearing loss in one family.
Human Genetics, Feb;112(2):156-163. Details

2003 Linge JP, Williams MA, Spronk CAEM, Bonvin AMJJ, Nilges M.
Refinement of protein structures in explicit solvent.
Proteins, Feb 15;50(3):496-506. Details

2003 Spronk CA, Nabuurs SB, Bonvin AM, Krieger E, Vuister GW, Vriend G.
The precision of NMR structure ensembles revisited.
Journal of Biomolecular NMR, Mar;25(3):225-234. Details

2003 Radenovic N, van Enckevort W, Verwer P, Vlieg E.
Growth and characteristics of the {111} NaCl crystal surface grown from solution.
Surface Science, 523:307-315. Details

2003 Travaille AM, Kaptijn L, Verwer P, Hulsken B, Elemans JA, Nolte RJ, van Kempen H.
Highly Oriented Self-Assembled Monolayers as Templates for Epitaxial Calcite Growth.
J Am Chem Soc, Sep 24;125(38):11571-11577. Details

2003 Oliveira L, Paiva PB, Paiva AC, Vriend G.
Identification of functionally conserved residues with the use of entropy-variability plots.
Proteins, Sep 1;52(4):544-552. Details

2003 Oliveira L, Paiva PB, Paiva AC, Vriend G.
Sequence analysis reveals how G protein-coupled receptors transduce the signal to the G protein.
Proteins, Sep 1;52(4):553-560. Details

2003 Gaseidnes S, Synstad B, Jia X, Kjellesvik H, Vriend G, Eijsink VG.
Stabilization of a chitinase from Serratia marcescens by Gly-->Ala and Xxx-->Pro mutations.
Protein Eng, Nov;16(11):841-846. Details

2003 van den Burg HA, Spronk CA, Boeren S, Kennedy M, Vissers H, Vuister GW, de Wit PJ, Vervoort J.
The interaction between the chitin-binding domain of the AVR4 elicitor of Cladosporium fulvum and chitin requires three occupied binding subsites.
Journal of Biological Chemistry, Apr 16;279(16):16786-16796 Details

2002 Duijf PH, Vanmolkot KR, Propping P, Friedl W, Krieger E, McKeon F, Dotsch V, Brunner HG, van Bokhoven H.
Gain-of-function mutation in ADULT syndrome reveals the presence of a second transactivation domain in p63.
Hum Mol Genet, Apr 1;11(7):799-804. Details

2002 Flohil JA, Vriend G, Berendsen HJ.
Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis.
Proteins, Sep 1;48(4):593-604. Details

2002 Geijtenbeek TB, van Duijnhoven GC, van Vliet SJ, Krieger E, Vriend G, Figdor CG, van Kooyk Y.
Identification of different binding sites in the dendritic cell-specific receptor DC-SIGN fpor ICAM-3 and HIV-1.
J Biol Chem, Mar 29;277(13):11314-11320. Details

2002 Klevering BJ, van Driel M, van Hogerwou AJ, van De Pol DJ, Deutman AF, Pinckers AJ, Cremers FP, Hoyng CB.
Central areolar choroidal dystrophy associated with dominantly inherited drusen.
Br J Ophthalmol, Jan;86(1):91-6. Details

2002 Kloks CP, Spronk CA, Lasonder E, Hoffmann A, Vuister GW, Grzesiek S, Hilbers CW.
The solution structure and DNA binding properties of the cold shock domain of the human Y-box protein YB-1.
J Mol Biol, Feb 15;316(2):317-326. Details

2002 Krieger E, Koraimann G, Vriend G.
Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field.
Proteins, May 15;47(3):393-402. Details

2002 de Kreij A, van den Burg B, Venema G, Vriend G, Eijsink VG, Nielsen JE.
The effects of modifying the surface charge on the catalytic activity of a thermolysin-like protease.
J Biol Chem, May 3;277(18):15432-15438. Details

2002 Krieger E, Vriend G.
Models@Home - distributed computing in bioinformatics using a screensaver based approach.
Bioinformatics, Feb;18(2):315-318. Details

2002 Leunissen JA, van Driel MA, Cuelenaere K, Neerincx P, Degenhart GH, Brunner HG.
Harvesting biological data using bioinformatics: Prediction of human disease genes.
Calcif Tissue Int, 70, 246.

2002 Oliveira L, Paiva AC, Vriend G.
Correlated mutation analyses on very large sequence families.
Chembiochem, Oct 4;3(10):1010-1017. Details

2002 Schulz HL, Stoehr H, White K, van Driel MA, Hoyng CB, Cremers F, Weber BH.
Genomic structure and assessment of the retinally expressed RFamide-related peptide gene in dominant cystoid macular dystrophy.
Molecular Vision , Mar 19;8:67-71. Details

2002 Singer MS, Vriend G, Bywater RP.
Prediction of protein residue contacts with a PDB-derived likelihood matrix.
Protein Eng, Sep;15(9):721-725. Details

2002 Spronk CA, Linge JP, Hilbers CW, Vuister GW.
Improving the quality of protein structures determined by NMR spectroscopy.
J Biomol NMR, Mar;22(3):281-289. Details

2002 Walma T, Spronk CA, Tessari M, Aelen J, Schepens J, Hendriks W, Vuister GW.
Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL.
Journal of Molecular Biology, Mar 8;316(5):1101-1110. Details

2001 Altenberg-Greulich B, Vriend G.
Where to attach dye molecules to a protein: lessons from WHAT IF.
J Mol Struc, 598:1-8. Details

2001 Bywater RP, Thomas D, Vriend G.
A sequence and structural study of transmembrane helices.
J Comput Aided Mol Des, Jun;15(6):533-552. Details

2001 Eijsink VGH, Vriend G, van den Burg B.
Engineering a hyperstable enzyme by manipulation of early steps in the unfolding process.
Biocat and Biotrans , 19(5-6):443-458. Details

2001 Horn F, Vriend G, Cohen FE.
Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems.
Nucleic Acids Res, Jan 1;29(1):346-349. Details

2001 Iconomidou VA, Chryssikos GD, Gionis V, Vriend G, Hoenger A, Hamodrakas SJ.
Amyloid-like fibrils from an 18-residue peptide analogue of a part of the central domain of the B-family of silkmoth chorion proteins.
FEBS Lett, Jun 22;499(3):268-273. Details

2001 de Kreij A, van den Burg B, Veltman OR, Vriend G, Venema G, Eijsink VG.
The effect of changing the hydrophobic S1' subsite of thermolysin-like protease substrate specificity.
Eur J Biochem, Sep;268(18):4985-4991. Details

2001 Kresse HP, Czubayko M, Nyakatura G, Vriend G, Sander C, Bloecker H.
Four-helix bundle topology re-engineered: monomeric Rop protein variants with different loop arrangements.
Protein Eng, Nov;14(11):897-901. Details

2001 Levashina EA, Moita LF, Blandin S, Vriend G, Lagueux M, Kafatos FC.
Conserved role of a complement-like protein in phagocytosis revealed by dsRNA knockout in cultured cells of the mosquito, Anopheles gambiae.
Cell, Mar 9;104(5):709-718. Details

2001 Nielsen JE, Borchert TV, Vriend G.
The determinants of alpha-amylase pH-activity profiles.
Protein Eng, Jul;14(7):505-512. Details

2001 Nielsen JE, Vriend G.
Optimizing the Hydrogen-Bond Network in Poisson-Boltzmann Equation-based pKa Calculations.
Proteins, Jun 1;43(4):403-412. Details

2001 Oliveira L, Vriend G, Paiva ACM.
A common ligand-binding site in G protein-coupled receptors.
Peptides for the new millennium, Edited by Fields, Tam, Barany. Kluwer, Dordrecht/Boston/London. pp 581-582.

2000 Brunner H, Cuelenaere K, Kemmeren P, van Driel M, Leunissen JA.
The Genemachine: A tool for the extraction and integration of information from web-based genetic databases.
Eur J Hum Gen, 8:Suppl. 1.

2000 Horn F, Mokrane M, Weare J, Vriend G.
G protein-coupled receptors, or the power of data.
Genomics and Proteomics: Functional and Computational Aspects, Edited by S. Suhai. Kluwer Academic / Plenum publishers, New York, pp. 191-214. Details

2000 Horn F, van der Wenden EM, Oliveira L, IJzerman AP, Vriend G.
Receptors coupling to G proteins: is there a signal behind the sequence?
Proteins, Dec 1;41(4):448-459. Details

2000 Iconomidou VA, Vriend G, Hamodrakas SJ.
Amyloids protect the silkmoth oocyte and embryo.
FEBS Lett, Aug 18;479(3):141-145. Details

2000 Tomilin A, Remenyi A, Lins K, Bak H, Leidel S, Vriend G, Wilmanns M, Scholer HR.
Synergism with the Coactivator OBF-1 (OCA-B, BOB-1) is Mediated by a Specific POU Dimer Configuration.
Cell , Dec 8;103(6):853-864. Details

1999 Williams JC, Zeelen JP, Neubauer G, Vriend G, Backmann J, Michels PA, Lambeir AM, Wierenga RK.
Structural and mutagenesis studies of leishmania triosephosphate isomerase: a point mutant can convert a mesophilic enzyme into a superstable enzyme without losing catalytic power.
Protein Eng, Mar;12(3):243-250. Details

1999 Boteva R, Visser AJ, Filippi B, Vriend G, Veenhuis M, van der Klei IJ.
Conformational transitions accompanying oligomerization of yeast alcohol oxidase, a peroxisomal flavoenzyme.
Biochemistry, Apr 20;38(16):5034-5044. Details

1999 Mansfeld J, Vriend G, Van den Burg B, Eijsink VG, Ulbrich-Hofmann R.
Probing the unfolding region in a thermolysin-like protease by site-specific immobilization.
Biochemistry, Jun 29;38(26):8240-8245. Details

1999 de Groot BL, Vriend G, Berendsen HJ.
Conformational changes in the chaperonin GRoEL: New insights into the allosteric mechanism.
J Mol Biol, Mar 5;286(4):1241-1249. Details

1999 Celli J, Duijf P, Hamel BC, Bamshad M, Kramer B, Smits AP, Newbury-Ecob R, Hennekam RC, Van Buggenhout G, van Haeringen A, Woods CG, van Essen AJ, de Waal R, Vriend G, Haber DA, Yang A, McKeon F, Brunner HG, van Bokhoven H.
Heterozygous Germline mutations in the p53 homolog p63 are the cause of EEC syndrome.
Cell, Oct 15;99(2):143-153. Details

1999 Dorelijers JF, Vriend G, Raves ML, Kaptein R.
Validation of NMR structures of proteins and nucleic acids: hydrogen geometry and nomenclature.
Proteins, Nov 15;37(3):404-416. Details

1999 Oliveira L, Paiva AC, Vriend G.
A low resolution model for the interaction of G proteins with G protein-coupled receptors.
Protein Eng, Dec;12(12):1087-1095. Details

1999 Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC.
Improving macromolecular electrostatics calculations.
Protein Eng, Aug;12(8):657-662. Details

1999 Rodriguez R, Chinea G, Lopez N, Vriend G.
Full window stereo.
J Mol Graph Model, Oct-Dec;17(5-6):310-4, 333. Details