Gert Vriend - Publications

 1989-1999 EMBL, Heidelberg, Baden-Württemberg, Germany 
 1999- Radboud University Nijmegen, Nijmegen, Gelderland, Netherlands 

158 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Krieger E, Vriend G. New ways to boost molecular dynamics simulations. Journal of Computational Chemistry. 36: 996-1007. PMID 25824339 DOI: 10.1002/jcc.23899  0.4
2015 Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, ... ... Vriend G, et al. Key challenges for the creation and maintenance of specialist protein resources. Proteins. 83: 1005-13. PMID 25820941 DOI: 10.1002/prot.24803  0.4
2015 Zarzycka B, Seijkens T, Nabuurs SB, Ritschel T, Grommes J, Soehnlein O, Schrijver R, van Tiel CM, Hackeng TM, Weber C, Giehler F, Kieser A, Lutgens E, Vriend G, Nicolaes GA. Discovery of small molecule CD40-TRAF6 inhibitors. Journal of Chemical Information and Modeling. 55: 294-307. PMID 25622654 DOI: 10.1021/ci500631e  0.4
2015 Lounnas V, Wedler HB, Newman T, Black J, Vriend G. Blind and visually impaired students can perform computer-aided molecular design with an assistive molecular fabricator Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9043: 18-29.  0.4
2014 Kwon TJ, Oh SK, Park HJ, Sato O, Venselaar H, Choi SY, Kim S, Lee KY, Bok J, Lee SH, Vriend G, Ikebe M, Kim UK, Choi JY. The effect of novel mutations on the structure and enzymatic activity of unconventional myosins associated with autosomal dominant non-syndromic hearing loss. Open Biology. 4. PMID 25080041 DOI: 10.1098/rsob.140107  0.4
2014 Krieger E, Vriend G. YASARA View - molecular graphics for all devices - from smartphones to workstations. Bioinformatics (Oxford, England). 30: 2981-2. PMID 24996895 DOI: 10.1093/bioinformatics/btu426  0.4
2014 Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, ... ... Vriend G, et al. PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Research. 42: W337-43. PMID 24799431 DOI: 10.1093/nar/gku366  1
2013 Joosten RP, Chinea G, Kleywegt GJ, Vriend G. Protein Three-Dimensional Structure Validation Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. DOI: 10.1016/B978-0-12-409547-2.02534-8  0.4
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. Biochemical Pharmacology. 84: 76-87. PMID 22449615 DOI: 10.1016/j.bcp.2012.03.008  1
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 Engineering, Design & Selection : Peds. 25: 39-46. PMID 22143875 DOI: 10.1093/protein/gzr057  1
2011 Read RJ, Adams PD, Arendall WB, 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, et al. A new generation of crystallographic validation tools for the protein data bank. Structure (London, England : 1993). 19: 1395-412. PMID 22000512 DOI: 10.1016/j.str.2011.08.006  0.48
2011 Eijsink VG, Matthews BW, Vriend G. The role of calcium ions in the stability and instability of a thermolysin-like protease. Protein Science : a Publication of the Protein Society. 20: 1346-55. PMID 21648000 DOI: 10.1002/pro.670  0.4
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. The Pharmacogenomics Journal. 11: 326-36. PMID 20531371 DOI: 10.1038/tpj.2010.44  1
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, ... ... Vriend G, et al. GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base. Bioinformatics (Oxford, England). 26: 1804-5. PMID 20501551 DOI: 10.1093/bioinformatics/btq264  1
2010 Venselaar H, Joosten RP, Vroling B, Baakman CA, Hekkelman ML, Krieger E, Vriend G. Homology modelling and spectroscopy, a never-ending love story. European Biophysics Journal : Ebj. 39: 551-63. PMID 19718498 DOI: 10.1007/s00249-009-0531-0  0.4
2009 Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, ... ... Vriend G, et al. PDB_REDO: automated re-refinement of X-ray structure models in the PDB. Journal of Applied Crystallography. 42: 376-384. PMID 22477769 DOI: 10.1107/S0021889809008784  0.4
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 Crystallographica. Section D, Biological Crystallography. 65: 176-85. PMID 19171973 DOI: 10.1107/S0907444908037591  0.4
2008 von Grotthuss M, Plewczynski D, Vriend G, Rychlewski L. 3D-Fun: predicting enzyme function from structure. Nucleic Acids Research. 36: W303-7. PMID 18515349 DOI: 10.1093/nar/gkn308  0.4
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 (London, England : 1993). 16: 747-54. PMID 18462679 DOI: 10.1016/j.str.2008.01.018  0.4
2008 Ye K, Vriend G, IJzerman AP. Tracing evolutionary pressure. Bioinformatics (Oxford, England). 24: 908-15. PMID 18304936 DOI: 10.1093/bioinformatics/btn057  0.4
2008 Collin RW, 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. 29: 545-54. PMID 18228599 DOI: 10.1002/humu.20693  0.4
2008 Collin RW, 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, ... ... Vriend G, et al. Mutations of ESRRB encoding estrogen-related receptor beta cause autosomal-recessive nonsyndromic hearing impairment DFNB35. American Journal of Human Genetics. 82: 125-38. PMID 18179891 DOI: 10.1016/j.ajhg.2007.09.008  0.4
2008 Vroling B, Vriend G. Harvesting the information from a family of proteins Modern Genome Annotation: the Biosapiens Network. 263-279. DOI: 10.1007/978-3-211-75123-7_13  0.4
2007 Joosten RP, Vriend G. PDB improvement starts with data deposition. Science (New York, N.Y.). 317: 195-6. PMID 17626865 DOI: 10.1126/science.317.5835.195  0.4
2007 Meijer JT, Roeters M, Viola V, Löwik DW, Vriend G, van Hest JC. Stabilization of peptide fibrils by hydrophobic interaction. Langmuir : the Acs Journal of Surfaces and Colloids. 23: 2058-63. PMID 17279695 DOI: 10.1021/la0625345  0.4
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. Molecular Endocrinology (Baltimore, Md.). 21: 30-48. PMID 17038419 DOI: 10.1210/me.2006-0072  1
2006 Paiva AC, Oliveira L, Horn F, Bywater RP, Vriend G. Modeling GPCRs. Ernst Schering Foundation Symposium Proceedings. 23-47. PMID 17703576  0.4
2006 Ott MA, Vriend G. Correcting ligands, metabolites, and pathways. Bmc Bioinformatics. 7: 517. PMID 17132165 DOI: 10.1186/1471-2105-7-517  0.4
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. Proceedings of the National Academy of Sciences of the United States of America. 103: 18089-94. PMID 17116887 DOI: 10.1073/pnas.0608909103  0.4
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, et al. Distinct clinical phenotypes associated with a mutation in the mitochondrial translation elongation factor EFTs. American Journal of Human Genetics. 79: 869-77. PMID 17033963 DOI: 10.1086/508434  0.4
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. The Journal of Biological Chemistry. 281: 40033-40. PMID 17032651 DOI: 10.1074/jbc.M603168200  0.4
2006 Krieger E, Nielsen JE, Spronk CA, Vriend G. Fast empirical pKa prediction by Ewald summation. Journal of Molecular Graphics & Modelling. 25: 481-6. PMID 16644253 DOI: 10.1016/j.jmgm.2006.02.009  0.4
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 Biochemistry and Molecular Biology. 36: 282-90. PMID 16551542 DOI: 10.1016/j.ibmb.2006.01.004  0.4
2006 Van Durme J, Horn F, Costagliola S, Vriend G, Vassart G. GRIS: glycoprotein-hormone receptor information system. Molecular Endocrinology (Baltimore, Md.). 20: 2247-55. PMID 16543405 DOI: 10.1210/me.2006-0020  0.4
2006 van Driel MA, Bruggeman J, Vriend G, Brunner HG, Leunissen JA. A text-mining analysis of the human phenome. European Journal of Human Genetics : Ejhg. 14: 535-42. PMID 16493445 DOI: 10.1038/sj.ejhg.5201585  0.4
2006 Nabuurs SB, Spronk CA, Vuister GW, Vriend G. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. Plos Computational Biology. 2: e9. PMID 16462939 DOI: 10.1371/journal.pcbi.0020009  0.4
2005 Nabuurs SB, Krieger E, Spronk CA, Nederveen AJ, Vriend G, Vuister GW. Definition of a new information-based per-residue quality parameter. Journal of Biomolecular Nmr. 33: 123-34. PMID 16258830 DOI: 10.1007/s10858-005-2826-5  0.4
2005 Hekkelman ML, Vriend G. MRS: a fast and compact retrieval system for biological data. Nucleic Acids Research. 33: W766-9. PMID 15980580 DOI: 10.1093/nar/gki422  0.4
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 Research. 33: W758-61. PMID 15980578 DOI: 10.1093/nar/gki435  0.4
2005 Folkertsma S, van Noort PI, Brandt RF, Bettler E, Vriend G, de Vlieg J. The nuclear receptor ligand-binding domain: a family-based structure analysis. Current Medicinal Chemistry. 12: 1001-16. PMID 15892635 DOI: 10.2174/0929867053764699  1
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. 59: 555-64. PMID 15778955 DOI: 10.1002/prot.20378  0.4
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. Applied and Environmental Microbiology. 71: 442-50. PMID 15640220 DOI: 10.1128/AEM.71.1.442-450.2005  0.4
2004 Vriend G. Protein design: quo vadis? Science (New York, N.Y.). 306: 1135. PMID 15539588 DOI: 10.1126/science.306.5699.1135a  0.4
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. 57: 678-83. PMID 15390263 DOI: 10.1002/prot.20251  0.4
2004 Eijsink VG, Bjørk A, Gåseidnes S, Sirevåg R, Synstad B, van den Burg B, Vriend G. Rational engineering of enzyme stability. Journal of Biotechnology. 113: 105-20. PMID 15380651 DOI: 10.1016/j.jbiotec.2004.03.026  0.4
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. Journal of Molecular Biology. 341: 321-35. PMID 15276826 DOI: 10.1016/j.jmb.2004.05.075  1
2004 Oliveira L, Hulsen T, Lutje Hulsik D, Paiva AC, Vriend G. Heavier-than-air flying machines are impossible. Febs Letters. 564: 269-73. PMID 15111108 DOI: 10.1016/S0014-5793(04)00320-5  1
2004 Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AM, Vuister GW, Vriend G, Spronk CA. DRESS: a database of REfined solution NMR structures. Proteins. 55: 483-6. PMID 15103611 DOI: 10.1002/prot.20118  0.4
2004 Le Guezennec X, Vriend G, Stunnenberg HG. Molecular determinants of the interaction of Mad with the PAH2 domain of mSin3. The Journal of Biological Chemistry. 279: 25823-9. PMID 15047710 DOI: 10.1074/jbc.M313860200  0.4
2004 Synstad B, Gåseidnes 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. European Journal of Biochemistry / Febs. 271: 253-62. PMID 14717693 DOI: 10.1046/j.1432-1033.2003.03923.x  0.4
2004 Spronk CAEM, Nabuurs SB, Krieger E, Vriend G, Vuister GW. Validation of protein structures derived by NMR spectroscopy Progress in Nuclear Magnetic Resonance Spectroscopy. 45: 315-337. DOI: 10.1016/j.pnmrs.2004.08.003  0.4
2004 Nabuurs SB, Spronk CAEM, Vriend G, Vuister GW. Concepts and tools for NMR restraint analysis and validation Concepts in Magnetic Resonance Part a: Bridging Education and Research. 22: 90-105. DOI: 10.1002/cmr.a.20016  0.4
2003 Gåseidnes 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 Engineering. 16: 841-6. PMID 14631073  0.4
2003 Campagne F, Bettler E, Vriend G, Weinstein H. Batch mode generation of residue-based diagrams of proteins. Bioinformatics (Oxford, England). 19: 1854-5. PMID 14512361 DOI: 10.1093/bioinformatics/btg236  0.4
2003 Nabuurs SB, Spronk CA, Krieger E, Maassen H, Vriend G, Vuister GW. Quantitative evaluation of experimental NMR restraints. Journal of the American Chemical Society. 125: 12026-34. PMID 14505424 DOI: 10.1021/ja035440f  0.4
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. 52: 553-60. PMID 12910455 DOI: 10.1002/prot.10489  1
2003 Oliveira L, Paiva PB, Paiva AC, Vriend G. Identification of functionally conserved residues with the use of entropy-variability plots. Proteins. 52: 544-52. PMID 12910454 DOI: 10.1002/prot.10490  1
2003 Bettler E, Krause R, Horn F, Vriend G. NRSAS: Nuclear Receptor Structure Analysis Servers. Nucleic Acids Research. 31: 3400-3. PMID 12824335 DOI: 10.1093/nar/gkg505  0.4
2003 Spronk CA, Nabuurs SB, Bonvin AM, Krieger E, Vuister GW, Vriend G. The precision of NMR structure ensembles revisited. Journal of Biomolecular Nmr. 25: 225-34. PMID 12652134 DOI: 10.1023/A:1022819716110  0.4
2003 Krieger E, Nabuurs SB, Vriend G. Homology modeling. Methods of Biochemical Analysis. 44: 509-23. PMID 12647402  0.4
2003 Van Durme JJ, Bettler E, Folkertsma S, Horn F, Vriend G. NRMD: Nuclear Receptor Mutation Database. Nucleic Acids Research. 31: 331-3. PMID 12520016 DOI: 10.1093/nar/gkg122  0.4
2003 Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G. GPCRDB information system for G protein-coupled receptors. Nucleic Acids Research. 31: 294-7. PMID 12520006 DOI: 10.1093/nar/gkg103  1
2002 Singer MS, Vriend G, Bywater RP. Prediction of protein residue contacts with a PDB-derived likelihood matrix. Protein Engineering. 15: 721-5. PMID 12456870  0.4
2002 Oliveira L, Paiva AC, Vriend G. Correlated mutation analyses on very large sequence families. Chembiochem : a European Journal of Chemical Biology. 3: 1010-7. PMID 12362367 DOI: 10.1002/1439-7633(20021004)3:10<1010::AID-CBIC1010>3.0.CO;2-T  0.4
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. 48: 593-604. PMID 12211026 DOI: 10.1002/prot.10105  0.4
2002 Krieger E, Koraimann G, Vriend G. Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field. Proteins. 47: 393-402. PMID 11948792 DOI: 10.1002/prot.10104  0.4
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. The Journal of Biological Chemistry. 277: 15432-8. PMID 11859085 DOI: 10.1074/jbc.M200807200  0.4
2002 Krieger E, Vriend G. Models@Home: distributed computing in bioinformatics using a screensaver based approach. Bioinformatics (Oxford, England). 18: 315-8. PMID 11847079  0.4
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 for intercellular adhesion molecule 3 and HIV-1. The Journal of Biological Chemistry. 277: 11314-20. PMID 11799126 DOI: 10.1074/jbc.M111532200  0.4
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 Engineering. 14: 897-901. PMID 11742109  1
2001 De Kreij A, Van Burg BD, Veltman OR, Vriend G, Venema G, Eijsink VGH. The effect of changing the hydrophobic S1′ subsite of thermolysin-like proteases on substrate specificity European Journal of Biochemistry. 268: 4985-4991. PMID 11559368 DOI: 10.1046/j.0014-2956.2001.02434.x  0.4
2001 Nielsen JE, Borchert TV, Vriend G. The determinants of alpha-amylase pH-activity profiles. Protein Engineering. 14: 505-12. PMID 11522925  1
2001 Bywater RP, Thomas D, Vriend G. A sequence and structural study of transmembrane helices Journal of Computer-Aided Molecular Design. 15: 533-552. PMID 11495225 DOI: 10.1023/A:1011197908960  0.4
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 Letters. 499: 268-273. PMID 11423129 DOI: 10.1016/S0014-5793(01)02510-8  0.4
2001 Nielsen JE, Vriend G. Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations. Proteins. 43: 403-12. PMID 11340657 DOI: 10.1002/prot.1053  1
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. 104: 709-18. PMID 11257225  0.4
2001 Horn F, Vriend G, Cohen FE. Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucleic Acids Research. 29: 346-9. PMID 11125133  1
2001 Eijsink VGH, Vriend G, Van Den Burg B. Engineering a hyperstable enzyme by manipulation of early steps in the unfolding process Biocatalysis and Biotransformation. 19: 443-458.  0.4
2001 Altenberg-Greulich B, Vriend G. Where to attach dye molecules to a protein: Lessons from the computer program WHAT IF Journal of Molecular Structure. 598: 1-8.  0.4
2000 Tomilin A, Reményi A, Lins K, Bak H, Leidel S, Vriend G, Wilmanns M, Schöler HR. Synergism with the coactivator OBF-1 (OCA-B, BOB-1) is mediated by a specific POU dimer configuration Cell. 103: 853-864. PMID 11136971  1
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: Structure, Function and Genetics. 41: 448-459. PMID 11056033 DOI: 10.1002/1097-0134(20001201)41:4<448::AID-PROT30>3.0.CO;2-C  0.4
2000 Iconomidou VA, Vriend G, Hamodrakas SJ. Amyloids protect the silkmoth oocyte and embryo Febs Letters. 479: 141-145. PMID 10981723 DOI: 10.1016/S0014-5793(00)01888-3  0.4
2000 Altenberg-Greulich B, Zech SG, Stehlik D, Vriend G. Physicist's simple access to protein structures: The computer program WHAT IF Proceedings of Spie - the International Society For Optical Engineering. 4430: 709-714. DOI: 10.1117/12.432914  0.4
1999 Rodriguez R, Chinea G, Lopez N, Vriend G. Full window stereo Journal of Molecular Graphics and Modelling. 17: 310-314+333. PMID 10840690 DOI: 10.1016/S1093-3263(99)00038-8  0.4
1999 Oliveira L, Paiva AC, Vriend G. A low resolution model for the interaction of G proteins with G protein-coupled receptors. Protein Engineering. 12: 1087-95. PMID 10611402  0.4
1999 Doreleijers JF, Vriend G, Raves ML, Kaptein R. Validation of nuclear magnetic resonance structures of proteins and nucleic acids: hydrogen geometry and nomenclature. Proteins. 37: 404-16. PMID 10591100 DOI: 10.1002/(SICI)1097-0134(19991115)37:3<404::AID-PROT8>3.0.CO;2-2  1
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, et al. Heterozygous germline mutations in the p53 homolog p63 are the cause of EEC syndrome. Cell. 99: 143-53. PMID 10535733 DOI: 10.1016/S0092-8674(00)81646-3  0.4
1999 Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC. Improving macromolecular electrostatics calculations. Protein Engineering. 12: 657-62. PMID 10469826  0.4
1999 Mansfeld J, Vriend G, Van Den Burg B, Eijsink VGH, Ulbrich-Hofmann R. Probing the unfolding region in a thermolysin-like protease by site- specific immobilization Biochemistry. 38: 8240-8245. PMID 10387069 DOI: 10.1021/bi990008p  0.4
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 mutation can convert a mesophilic enzyme into a superstable enzyme without losing catalytic power. Protein Engineering. 12: 243-50. PMID 10235625  0.4
1999 Boteva R, Visser AJWG, Filippi B, Vriend G, Veenhuis M, Van Der Klei IJ. Conformational transitions accompanying oligomerization of yeast alcohol oxidase, a peroxisomal flavoenzyme Biochemistry. 38: 5034-5044. PMID 10213606 DOI: 10.1021/bi982266c  0.4
1999 de Groot BL, Vriend G, Berendsen HJ. Conformational changes in the chaperonin GroEL: new insights into the allosteric mechanism. Journal of Molecular Biology. 286: 1241-9. PMID 10047494 DOI: 10.1006/jmbi.1998.2568  1
1998 Vriend G, Berendsen HJ, van den Burg B, Venema G, Eijsink VG. Early steps in the unfolding of thermolysin-like proteases. The Journal of Biological Chemistry. 273: 35074-7. PMID 9857041 DOI: 10.1074/jbc.273.52.35074  1
1998 Rodriguez R, Chinea G, Lopez N, Pons T, Vriend G. Homology modeling, model and software evaluation: Three related resources Bioinformatics. 14: 523-528. PMID 9694991 DOI: 10.1093/bioinformatics/14.6.523  0.4
1998 Horn F, Bywater R, Krause G, Kuipers W, Oliveira L, Paiva AC, Sander C, Vriend G. The interaction of class B G protein-coupled receptors with their hormones. Receptors & Channels. 5: 305-14. PMID 9666522  0.4
1998 Horn F, Vriend G. G protein-coupled receptors in silico Journal of Molecular Medicine. 76: 464-468. PMID 9660164 DOI: 10.1007/s001090050240  1
1998 Botquin V, Hess H, Fuhrmann G, Anastassiadis C, Gross MK, Vriend G, Schöler HR. New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2 Genes and Development. 12: 2073-2090. PMID 9649510  1
1998 Van Den Burg B, Eijsink VGH, Vriend G, Veltman OR, Venema G. Rendering one autolysis site in Bacillus subtilis neutral protease resistant to cleavage reveals a new fission Biotechnology and Applied Biochemistry. 27: 125-132. PMID 9569607  0.4
1998 Veltman OR, Vriend G, Berendsen HJ, Van den Burg B, Venema G, Eijsink VG. A single calcium binding site is crucial for the calcium-dependent thermal stability of thermolysin-like proteases. Biochemistry. 37: 5312-9. PMID 9548763 DOI: 10.1021/bi9725879  0.4
1998 Veltman OR, Eijsink VGH, Vriend G, De Kreij A, Venema G, Van Den Burg B. Probing catalytic hinge bending motions in thermolysin-like proteases by Glycine → Alanine mutations Biochemistry. 37: 5305-5311. PMID 9548762 DOI: 10.1021/bi972374j  0.4
1998 Steinberger D, Vriend G, Mulliken JB, Müller U. The mutations in FGFR2-associated craniosynostoses are clustered in five structural elements of immunoglobulin-like domain III of the receptor Human Genetics. 102: 145-150. PMID 9521581 DOI: 10.1007/s004390050668  0.4
1998 Wilson KS, Butterworth S, Dauter Z, Lamzin VS, Walsh M, Wodak S, Pontius J, Richelle J, Vaguine A, Sander C, Hooft RWW, Vriend G, Thornton JM, Laskowski RA, MacArthur MW, et al. Who checks the checkers? Four validation tools applied to eight atomic resolution structures Journal of Molecular Biology. 276: 417-436. PMID 9512713 DOI: 10.1006/jmbi.1997.1526  1
1998 Van Den Burg B, Vriend G, Veltman OR, Venema G, Eijsink VGH. Engineering an enzyme to resist boiling Proceedings of the National Academy of Sciences of the United States of America. 95: 2056-2060. PMID 9482837 DOI: 10.1073/pnas.95.5.2056  0.4
1998 Horn F, Weare J, Beukers MW, Hörsch S, Bairoch A, Chen W, Edvardsen, Campagne F, Vriend G. GPCRDB: An information system for G protein-coupled receptors Nucleic Acids Research. 26: 275-279. PMID 9399852 DOI: 10.1093/nar/26.1.275  0.4
1998 Mansfeld J, Vriend G, Burg BVd, Venema G, Eijsink VGH, Ulbrich-Hofmann R. The effect of site-specific immobilization on the thermal stability of thermolysin-like neutral proteases Progress in Biotechnology. 15: 513-516. DOI: 10.1016/S0921-0423(98)80076-2  1
1997 Kuipers W, Oliveira L, Vriend G, Uzerman AP. Identification of class-determining residues in G protein-coupled receptors by sequence analysis Receptors and Channels. 5: 159-174. PMID 9606720  0.4
1997 Sobolev V, Moallem TM, Wade RC, Vriend G, Edelman M. CASP2 molecular docking predictions with the LIGIN software Proteins: Structure, Function and Genetics. 29: 210-214. PMID 9485514 DOI: 10.1002/(SICI)1097-0134(1997)1+<210::AID-PROT28>3.0.CO;2-Q  0.4
1997 Veltman OR, Vriend G, Hardy F, Mansfeld J, Van Den Burg B, Venema G, Eijsink VGH. Mutational analysis of a surface area that is critical for the thermal stability of thermolysin-like proteases European Journal of Biochemistry. 248: 433-440. PMID 9346299  0.4
1997 de Groot BL, van Aalten DM, Scheek RM, Amadei A, Vriend G, Berendsen HJ. Prediction of protein conformational freedom from distance constraints. Proteins. 29: 240-51. PMID 9329088 DOI: 10.1002/(SICI)1097-0134(199710)29:2<240::AID-PROT11>3.0.CO;2-O  0.4
1997 Vincentz M, Leite A, Neshich G, Vriend G, Mattar C, Barros L, Weinberg D, De Almeida ER, Paes De Carvalho M, Aragão F, Gander ES. ACGT and vicilin core sequences in a promoter domain required for seed-specific expression of a 2S storage protein gene are recognized by the opaque-2 regulatory protein Plant Molecular Biology. 34: 879-889. PMID 9290640 DOI: 10.1023/A:1005874404706  0.4
1997 Hooft RWW, Sander C, Vriend G. Objectively judging the quality of a protein structure from a Ramachandran plot Computer Applications in the Biosciences. 13: 425-430. PMID 9283757  1
1997 de Freitas SM, de Mello LV, da Silva MC, Vriend G, Neshich G, Ventura MM. Analysis of the black-eyed pea trypsin and chymotrypsin inhibitor-alpha-chymotrypsin complex. Febs Letters. 409: 121-7. PMID 9202130 DOI: 10.1016/S0014-5793(97)00419-5  1
1997 Frigerio F, Margarit I, Nogarotto R, Grandi G, Vriend G, Hardy F, Veltman OR, Venema G, Eijsink VGH. Model building of a thermolysin-like protease by mutagenesis Protein Engineering. 10: 223-230. PMID 9153087  0.4
1997 Mansfeld J, Vriend G, Dijkstra BW, Veltman OR, Van Den Burg B, Venema G, Ulbrich-Hofmann R, Eijsink VGH. Extreme stabilization of a thermolysin-like protease by an engineered disulfide bond Journal of Biological Chemistry. 272: 11152-11156. PMID 9111013 DOI: 10.1074/jbc.272.17.11152  0.4
1997 Veltman OR, Vriend G, Van Den Burg B, Hardy F, Venema G, Eijsink VGH. Engineering thermolysin-like proteases whose stability is largely independent of calcium Febs Letters. 405: 241-244. PMID 9089298 DOI: 10.1016/S0014-5793(97)00193-2  0.4
1997 Van Burg Rung B, Eijsink V, Vriend G, Veltman R, Venema G. Manipulating bacillus neutral protease autolysis Protein Engineering. 10: 37.  0.4
1997 Veltman OR, Eijsink VGH, Vriend G, Venema G, Van Den Burg B. Identification of the critical calcium site in the thermolysin-like protease of B. stearothermophilus reveals initial steps in thermal unfolding Protein Engineering. 10: 37.  0.4
1996 Hooft RWW, Sander C, Scharf M, Vriend G. The PDBFINDER database: A summary of PDB, DSSP and HSSP information with added value Computer Applications in the Biosciences. 12: 525-529. PMID 9021272  1
1996 Veltman OR, Vriend G, Middelhoven PJ, Van den Burg B, Venema G, Eijsink VGH. Analysis of structural determinants of the stability of thermolysin-like proteases by molecular modelling and site-directed mutagenesis Protein Engineering. 9: 1181-1189. PMID 9010931  0.4
1996 Hooft RWW, Sander C, Vriend G. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures Proteins: Structure, Function and Genetics. 26: 363-376. PMID 8990493 DOI: 10.1002/(SICI)1097-0134(199612)26:4<363::AID-PROT1>3.0.CO;2-D  1
1996 Hooft RWW, Vriend G. Improved coordinate reconstruction from stereo diagrams Journal of Molecular Graphics. 14: 168-172. PMID 8901644 DOI: 10.1016/S0263-7855(96)00055-0  1
1996 Sobolev V, Wade RC, Vriend G, Edelman M. Molecular docking using surface complementarity Proteins: Structure, Function and Genetics. 25: 120-129. PMID 8727324 DOI: 10.1002/(SICI)1097-0134(199605)25:1<120::AID-PROT10>3.0.CO;2-M  0.4
1996 Hooft RWW, Vriend G, Sander C, Abola EE. Errors in protein structures [3] Nature. 381: 272. PMID 8692262  0.4
1996 Hooft RWW, Sander C, Vriend G. Verification of Protein Structures: Side-Chain Planarity Journal of Applied Crystallography. 29: 714-716.  1
1995 Chinea G, Padron G, Hooft RWW, Sander C, Vriend G. The use of position-specific rotamers in model building by homology Proteins: Structure, Function and Genetics. 23: 415-421. PMID 8710834 DOI: 10.1002/prot.340230315  0.4
1995 Singer MS, Oliveira L, Vriend G, Shepherd GM. Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis. Receptors & Channels. 3: 89-95. PMID 8581404  0.4
1995 Dunkel R, Vriend G, Beato M, Suske G. Progesterone binding to uteroglobin: two alternative orientations of the ligand. Protein Engineering. 8: 71-9. PMID 7770456  0.4
1995 van Aalten DM, Amadei A, Linssen AB, Eijsink VG, Vriend G, Berendsen HJ. The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water. Proteins. 22: 45-54. PMID 7675786 DOI: 10.1002/prot.340220107  0.4
1995 Eijsink VGH, Veltman OR, Aukema W, Vriend G, Venema G. Structural determinants of the stability of thermolysin-like proteinases Nature Structural Biology. 2: 374-379. PMID 7664094 DOI: 10.1038/nsb0595-374  0.4
1995 Goossens F, De Meester I, Vanhoof G, Hendriks D, Vriend G, Scharpe S. The purification, characterization and analysis of primary and secondary-structure of prolyl oligopeptidase from human lymphocytes - Evidence that the enzyme belongs to the α/β hydrolase fold family European Journal of Biochemistry. 233: 432-441. PMID 7588785  0.4
1994 Hardy F, Vriend G, Van der Vinne B, Frigerio F, Grandi G, Venema G, Eijsink VGH. The effect of engineering surface loops on the thermal stability of Bacillus subtilis neutral protease Protein Engineering. 7: 425-430. PMID 8177891  0.4
1994 Van den Burg B, Dijkstra BW, Vriend G, Van der Vinne B, Venema G, Eijsink VGH. Protein stabilization by hydrophobic interactions at the surface European Journal of Biochemistry. 220: 981-985. PMID 8143751  0.4
1994 Vriend G, Sander C, Stouten PFW. A novel search method for protein sequence-structure relations using property profiles Protein Engineering. 7: 23-29. PMID 8140091  1
1994 Oliveira L, Paiva AC, Sander C, Vriend G. A common step for signal transduction in G protein-coupled receptors. Trends in Pharmacological Sciences. 15: 170-2. PMID 8091507 DOI: 10.1016/0165-6147(94)90137-6  0.4
1994 Vanhoof G, Goossens F, Hendriks L, De Meester I, Hendriks D, Vriend G, Van Broeckhoven C, Scharpé S. Cloning and sequence analysis of the gene encoding human lymphocyte prolyl endopeptidase Gene. 149: 363-366. PMID 7959018 DOI: 10.1016/0378-1119(94)90177-5  1
1993 Hardy F, Vriend G, Veltman OR, van der Vinne B, Venema G, Eijsink VGH. Stabilization of Bacillus stearothermophilus neutral protease by introduction of prolines Febs Letters. 317: 89-92. PMID 8428638 DOI: 10.1016/0014-5793(93)81497-N  1
1993 Keaveney M, Berkenstam A, Feigenbutz M, Vriend G, Stunnenberg HG. Residues in the TATA-binding protein required to mediate a transcriptional response to retinoic acid in EC cells Nature. 365: 562-566. PMID 8413615  1
1993 Hendriks D, Vingron M, Vriend G, Wang W, Nalis D, Scharpé S. On the Specificity of Carboxypeptidase N, a Comparative Study Biological Chemistry Hoppe-Seyler. 374: 843-850. PMID 8267877 DOI: 10.1515/bchm3.1993.374.7-12.843  1
1993 Vriend G, Eijsink V. Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases Journal of Computer-Aided Molecular Design. 7: 367-396. PMID 8229092 DOI: 10.1007/BF02337558  0.4
1993 Vriend G, Sander C. Quality control of protein models: Directional atomic contact analysis Journal of Applied Crystallography. 26: 47-60. DOI: 10.1107/S0021889892008240  1
1993 Oliveira L, Paiva ACM, Vriend G. A common motif in G-protein-coupled seven transmembrane helix receptors Journal of Computer-Aided Molecular Design. 7: 649-658. DOI: 10.1007/BF00125323  0.4
1992 Eijsink VG, Vriend G, Van der Zee JR, Van den Burg B, Venema G. Increasing the thermostability of the neutral proteinase of Bacillus stearothermophilus by improvement of internal hydrogen-bonding. The Biochemical Journal. 285: 625-8. PMID 1637352 DOI: 10.1042/bj2850625  0.4
1992 Sander C, Vriend G, Bazan F, Horovitz A, Nakamura H, Ribas L, Finkelstein AV, Lockhart A, Merkl R, Perry LJ. Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida. Proteins. 12: 105-10. PMID 1603799 DOI: 10.1002/prot.340120203  0.4
1992 Eijsink VG, Vriend G, van den Burg B, van der Zee JR, Venema G. Increasing the thermostability of a neutral protease by replacing positively charged amino acids in the N-terminal turn of alpha-helices. Protein Engineering. 5: 165-70. PMID 1594571 DOI: 10.1093/protein/5.2.165  0.4
1992 Eijsink VG, Vriend G, van den Burg B, van der Zee JR, Veltman OR, Stulp BK, Venema G. Introduction of a stabilizing 10 residue beta-hairpin in Bacillus subtilis neutral protease. Protein Engineering. 5: 157-63. PMID 1594570 DOI: 10.1093/protein/5.2.157  0.4
1992 Eijsink VG, Dijkstra BW, Vriend G, van der Zee JR, Veltman OR, van der Vinne B, van den Burg B, Kempe S, Venema G. The effect of cavity-filling mutations on the thermostability of Bacillus stearothermophilus neutral protease. Protein Engineering. 5: 421-6. PMID 1518790 DOI: 10.1093/protein/5.5.421  0.48
1992 Eijsink VG, Vriend G, van der Vinne B, Hazes B, van den Burg B, Venema G. Effects of changing the interaction between subdomains on the thermostability of Bacillus neutral proteases. Proteins. 14: 224-36. PMID 1409570 DOI: 10.1002/prot.340140209  0.4
1991 Wierenga RK, Noble MEM, Vriend G, Nauche S, Hol WGJ. Refined 1.83 Å structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 m-ammonium sulphate. A comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3-phosphate complex Journal of Molecular Biology. 220: 995-1015. PMID 1880808 DOI: 10.1016/0022-2836(91)90368-G  1
1991 Vriend G, Berendsen HJ, van der Zee JR, van den Burg B, Venema G, Eijsink VG. Stabilization of the neutral protease of Bacillus stearothermophilus by removal of a buried water molecule. Protein Engineering. 4: 941-5. PMID 1817257  0.4
1989 Schierbeek AJ, Swarte MB, Dijkstra BW, Vriend G, Read RJ, Hol WG, Drenth J, Betzel C. X-ray structure of lipoamide dehydrogenase from Azotobacter vinelandii determined by a combination of molecular and isomorphous replacement techniques. Journal of Molecular Biology. 206: 365-79. PMID 2716052 DOI: 10.1016/0022-2836(89)90486-5  1
1989 Luo M, Vriend G, Kamer G, Rossmann MG. Structure determination of Mengo virus. Acta Crystallographica. Section B, Structural Science. 45: 85-92. PMID 2559754 DOI: 10.1107/s0108768188010894  0.56
1989 Schreuder HA, Prick PA, Wierenga RK, Vriend G, Wilson KS, Hol WG, Drenth J. Crystal structure of the p-hydroxybenzoate hydroxylase-substrate complex refined at 1.9 A resolution. Analysis of the enzyme-substrate and enzyme-product complexes. Journal of Molecular Biology. 208: 679-96. PMID 2553983 DOI: 10.1016/0022-2836(89)90158-7  1
1989 Voorintholt R, Kosters MT, Vegter G, Vriend G, Hol WG. A very fast program for visualizing protein surfaces, channels and cavities. Journal of Molecular Graphics. 7: 243-5. PMID 2486827 DOI: 10.1016/0263-7855(89)80010-4  0.76
1987 Arnold E, Luo M, Vriend G, Rossmann MG, Palmenberg AC, Parks GD, Nicklin MJ, Wimmer E. Implications of the picornavirus capsid structure for polyprotein processing Proceedings of the National Academy of Sciences of the United States of America. 84: 21-25. PMID 3467351 DOI: 10.1073/pnas.84.1.21  0.4
1987 Luo M, Vriend G, Kamer G, Minor I, Arnold E, Rossmann MG, Boege U, Scraba DG, Duke GM, Palmenberg AC. The atomic structure of Mengo virus at 3.0 A resolution. Science (New York, N.Y.). 235: 182-91. PMID 3026048 DOI: 10.1126/science.3026048  0.56
1987 Blaas D, Kuechler E, Vriend G, Arnold E, Luo M, Rossmann MG. Comparison of the three-dimensional structure of two human rhinoviruses (HRV2 and HRV14). Proteins. 2: 263-72. PMID 2834716 DOI: 10.1002/prot.340020402  0.56
1986 Vriend G, Verduin BJM, Hemminga MA. Role of the N-terminal part of the coat protein in the assembly of cowpea chlorotic mottle virus. A 500 MHz proton nuclear magnetic resonance study and structural calculations Journal of Molecular Biology. 191: 453-460. PMID 3820293 DOI: 10.1016/0022-2836(86)90140-3  1
1986 Smith TJ, Kremer MJ, Luo M, Vriend G, Arnold E, Kamer G, Rossmann MG, McKinlay MA, Diana GD, Otto MJ. The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating. Science (New York, N.Y.). 233: 1286-93. PMID 3018924  0.56
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