| Year |
Citation |
Score |
| 2019 |
Lange J, Baakman C, Pistorius A, Krieger E, Hooft R, Joosten R, Vriend G. Facilities that make the PDB data collection more powerful. Protein Science : a Publication of the Protein Society. PMID 31724231 DOI: 10.1002/Pro.3788 |
0.371 |
|
| 2019 |
Shalaeva DN, Cherepanov DA, Galperin MY, Vriend G, Mulkidjanian AY. G protein-coupled receptors of class A harness the energy of membrane potential to increase their sensitivity and selectivity. Biochimica Et Biophysica Acta. Biomembranes. 183051. PMID 31449800 DOI: 10.1016/J.Bbamem.2019.183051 |
0.32 |
|
| 2018 |
Shirvanizadeh N, Vriend G, Arab SS. Loop modelling 1.0. Journal of Molecular Graphics & Modelling. 84: 64-68. PMID 29920424 DOI: 10.1016/J.Jmgm.2018.06.001 |
0.302 |
|
| 2018 |
Wozniak PP, Pelc J, Skrzypecki M, Vriend G, Kotulska M. Bio-knowledge-based filters improve residue-residue contact prediction accuracy. Bioinformatics (Oxford, England). 34: 3675-3683. PMID 29850768 DOI: 10.1093/Bioinformatics/Bty416 |
0.313 |
|
| 2018 |
Kooistra AJ, Vass M, McGuire R, Leurs R, de Esch IJ, Vriend G, Verhoeven S, de Graaf C. 3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery. Chemmedchem. PMID 29337438 DOI: 10.1002/Cmdc.201700754 |
0.342 |
|
| 2018 |
Singh D, Berntsen KRM, Baakman C, Vriend G, Lahiri T. A Critical Note on Symmetry Contact Artifacts and the Evaluation of the Quality of Homology Models Symmetry. 10: 25. DOI: 10.3390/Sym10010025 |
0.366 |
|
| 2017 |
Wozniak PP, Konopka BM, Xu J, Vriend G, Kotulska M. Forecasting residue-residue contact prediction accuracy. Bioinformatics (Oxford, England). PMID 29036497 DOI: 10.1093/Bioinformatics/Btx416 |
0.317 |
|
| 2017 |
van den Bergh T, Tamo G, Nobili A, Tao Y, Tan T, Bornscheuer UT, Kuipers RKP, Vroling B, de Jong RM, Subramanian K, Schaap PJ, Desmet T, Nidetzky B, Vriend G, Joosten HJ. CorNet: Assigning function to networks of co-evolving residues by automated literature mining. Plos One. 12: e0176427. PMID 28545124 DOI: 10.1371/Journal.Pone.0176427 |
0.357 |
|
| 2017 |
Schwarte A, Genz M, Skalden L, Nobili A, Vickers C, Melse O, Kuipers R, Joosten HJ, Stourac J, Bendl J, Black J, Haase P, Baakman C, Damborsky J, Bornscheuer U, ... Vriend G, et al. NewProt - a protein engineering portal. Protein Engineering, Design & Selection : Peds. 1-7. PMID 28475759 DOI: 10.1093/Protein/Gzx024 |
0.34 |
|
| 2017 |
Wozniak PP, Vriend G, Kotulska M. Correlated mutations select misfolded from properly folded proteins. Bioinformatics (Oxford, England). 33: 1497-1504. PMID 28203707 DOI: 10.1093/Bioinformatics/Btx013 |
0.368 |
|
| 2016 |
Munk C, Isberg V, Mordalski S, Harpsøe K, Rataj K, Hauser AS, Kolb P, Bojarski AJ, Vriend G, Gloriam DE. GPCRdb: the G protein-coupled receptor database - an introduction. British Journal of Pharmacology. 173: 2195-207. PMID 27155948 DOI: 10.1111/Bph.13509 |
0.34 |
|
| 2016 |
Vollan HS, Tannæs T, Vriend G, Bukholm G. In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality. International Journal of Molecular Sciences. 17. PMID 27110766 DOI: 10.3390/Ijms17040599 |
0.327 |
|
| 2016 |
Touw WG, Joosten RP, Vriend G. New biological insights from better structure models. Journal of Molecular Biology. PMID 26869101 DOI: 10.1016/J.Jmb.2016.02.002 |
0.347 |
|
| 2015 |
Lange J, Wyrwicz LS, Vriend G. KMAD: Knowledge based multiple sequence alignment for intrinsically disordered proteins. Bioinformatics (Oxford, England). PMID 26568635 DOI: 10.1093/Bioinformatics/Btv663 |
0.336 |
|
| 2015 |
Zarzycka B, Kuenemann MA, Miteva MA, Nicolaes GA, Vriend G, Sperandio O. Stabilization of protein-protein interaction complexes through small molecules. Drug Discovery Today. PMID 26434617 DOI: 10.1016/J.Drudis.2015.09.011 |
0.309 |
|
| 2015 |
Labbé CM, Kuenemann MA, Zarzycka B, Vriend G, Nicolaes GA, Lagorce D, Miteva MA, Villoutreix BO, Sperandio O. iPPI-DB: an online database of modulators of protein-protein interactions. Nucleic Acids Research. PMID 26432833 DOI: 10.1093/Nar/Gkv982 |
0.338 |
|
| 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 |
0.315 |
|
| 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 |
0.302 |
|
| 2014 |
van der Kant R, Vriend G. Alpha-bulges in G protein-coupled receptors. International Journal of Molecular Sciences. 15: 7841-64. PMID 24806342 DOI: 10.3390/Ijms15057841 |
0.303 |
|
| 2014 |
Berntsen KR, Vriend G. Anomalies in the refinement of isoleucine. Acta Crystallographica. Section D, Biological Crystallography. 70: 1037-49. PMID 24699648 DOI: 10.1107/S139900471400087X |
0.33 |
|
| 2013 |
Venselaar H, Camilli F, Gholizadeh S, Snelleman M, Brunner HG, Vriend G. Status quo of annotation of human disease variants. Bmc Bioinformatics. 14: 352. PMID 24305467 DOI: 10.1186/1471-2105-14-352 |
0.337 |
|
| 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. Journal of Biomolecular Nmr. 54: 267-83. PMID 22986687 DOI: 10.1007/S10858-012-9669-7 |
0.322 |
|
| 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. Journal of Molecular Medicine (Berlin, Germany). 90: 1321-31. PMID 22610276 DOI: 10.1007/S00109-012-0911-2 |
0.32 |
|
| 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: e33931. PMID 22606222 DOI: 10.1371/Journal.Pone.0033931 |
0.335 |
|
| 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 Research. 40: D519-24. PMID 22139937 DOI: 10.1093/Nar/Gkr1134 |
0.314 |
|
| 2012 |
Meyer T, Hensen U, Haas J, Rex R, Vriend G, Grubmüller H. The Dynasome as the Missing Link Between Protein Structure and Function Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.2465 |
0.348 |
|
| 2011 |
Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A. Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank. Bioinformatics (Oxford, England). 27: 3392-8. PMID 22034521 DOI: 10.1093/Bioinformatics/Btr590 |
0.366 |
|
| 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 |
0.32 |
|
| 2011 |
Joosten RP, te Beek TA, Krieger E, Hekkelman ML, Hooft RW, Schneider R, Sander C, Vriend G. A series of PDB related databases for everyday needs. Nucleic Acids Research. 39: D411-9. PMID 21071423 DOI: 10.1093/Nar/Gkq1105 |
0.368 |
|
| 2010 |
Venselaar H, Te Beek TA, Kuipers RK, Hekkelman ML, Vriend G. Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. Bmc Bioinformatics. 11: 548. PMID 21059217 DOI: 10.1186/1471-2105-11-548 |
0.345 |
|
| 2010 |
Hekkelman ML, Te Beek TA, Pettifer SR, Thorne D, Attwood TK, Vriend G. WIWS: a protein structure bioinformatics Web service collection. Nucleic Acids Research. 38: W719-23. PMID 20501602 DOI: 10.1093/Nar/Gkq453 |
0.313 |
|
| 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. 78: 2101-13. PMID 20455266 DOI: 10.1002/Prot.22725 |
0.358 |
|
| 2010 |
Huberts DH, Venselaar H, Vriend G, Veenhuis M, van der Klei IJ. The moonlighting function of pyruvate carboxylase resides in the non-catalytic end of the TIM barrel. Biochimica Et Biophysica Acta. 1803: 1038-42. PMID 20359504 DOI: 10.1016/J.Bbamcr.2010.03.018 |
0.321 |
|
| 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. 5: 455-67. PMID 20104563 DOI: 10.1002/Cmdc.200900461 |
0.323 |
|
| 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 |
0.329 |
|
| 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. Journal of Biomolecular Nmr. 45: 389-96. PMID 19809795 DOI: 10.1007/S10858-009-9378-Z |
0.325 |
|
| 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. Physiological Genomics. 39: 195-201. PMID 19671658 DOI: 10.1152/Physiolgenomics.00100.2009 |
0.339 |
|
| 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. 76: 608-16. PMID 19274741 DOI: 10.1002/Prot.22374 |
0.322 |
|
| 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 |
0.333 |
|
| 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 |
0.313 |
|
| 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 |
0.324 |
|
| 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 |
0.311 |
|
| 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 |
0.333 |
|
| 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 |
0.448 |
|
| 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 |
0.317 |
|
| 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 |
0.308 |
|
| 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 |
0.362 |
|
| 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 |
0.307 |
|
| 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 |
0.327 |
|
| 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 |
0.334 |
|
| 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 |
0.333 |
|
| 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 |
0.47 |
|
| 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 |
0.333 |
|
| 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 |
0.324 |
|
| 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 |
0.324 |
|
| 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 |
0.311 |
|
| 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 |
0.326 |
|
| 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 |
0.325 |
|
| 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 DOI: 10.1093/Protein/15.9.721 |
0.375 |
|
| 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 |
0.581 |
|
| 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 |
0.447 |
|
| 2001 |
Nielsen JE, Borchert TV, Vriend G. The determinants of alpha-amylase pH-activity profiles. Protein Engineering. 14: 505-12. PMID 11522925 DOI: 10.1093/Protein/14.7.505 |
0.342 |
|
| 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 |
0.346 |
|
| 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 DOI: 10.1016/S0092-8674(01)00267-7 |
0.311 |
|
| 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. DOI: 10.3109/10242420108992029 |
0.314 |
|
| 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 DOI: 10.1093/Protein/12.8.657 |
0.362 |
|
| 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 DOI: 10.1093/Protein/12.3.243 |
0.575 |
|
| 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 |
0.304 |
|
| 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 |
0.556 |
|
| 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 |
0.585 |
|
| 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 |
0.516 |
|
| 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 |
0.302 |
|
| 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 |
0.329 |
|
| 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 |
0.34 |
|
| 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 DOI: 10.1111/J.1432-1033.1997.00433.X |
0.308 |
|
| 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 |
0.6 |
|
| 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 |
0.321 |
|
| 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 DOI: 10.1093/Bioinformatics/12.6.525 |
0.336 |
|
| 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 DOI: 10.1093/Protein/9.12.1181 |
0.347 |
|
| 1996 |
Aalten DMFv, Bywater R, Findlay JBC, Hendlich M, Hooft RWW, Vriend G. PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design. 10: 255-262. PMID 8808741 DOI: 10.1007/Bf00355047 |
0.305 |
|
| 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 |
0.327 |
|
| 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 DOI: 10.1093/Protein/8.1.71 |
0.31 |
|
| 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 |
0.538 |
|
| 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 DOI: 10.1111/J.1432-1033.1994.Tb18702.X |
0.33 |
|
| 1994 |
Rodenburg KW, Scheeren-Groot E, Vriend G, Hooykaas PJ. The N-terminal domain of VirG of Agrobacterium tumefaciens: modelling and analysis of mutant phenotypes. Protein Engineering. 7: 905-9. PMID 7971952 DOI: 10.1093/Protein/7.7.905 |
0.304 |
|
| 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 |
0.361 |
|
| 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 |
0.307 |
|
| 1992 |
Peter W, Dunkel R, Stouten PF, Vriend G, Beato M, Suske G. Interchain cysteine bridges control entry of progesterone to the central cavity of the uteroglobin dimer. Protein Engineering. 5: 351-9. PMID 1409556 DOI: 10.1093/Protein/5.4.351 |
0.329 |
|
| 1992 |
Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G. A database of protein structure families with common folding motifs Protein Science. 1: 1691-1698. PMID 1304898 DOI: 10.1002/Pro.5560011217 |
0.375 |
|
| 1991 |
Peter W, Brüller HJ, Vriend G, Beato M, Suske G. Identification of residues essential for progesterone binding to uteroglobin by site-directed mutagenesis. The Journal of Steroid Biochemistry and Molecular Biology. 38: 27-33. PMID 1997121 DOI: 10.1016/0960-0760(91)90397-N |
0.344 |
|
| 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 |
0.544 |
|
| 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 |
0.576 |
|
| 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 |
0.618 |
|
| 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 |
0.395 |
|
| 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 |
0.683 |
|
| 1989 |
Kowalski H, Maurer-Fogy I, Vriend G, Casari G, Beyer A, Blaas D. Trypsin sensitivity of several human rhinovirus serotypes in their low pH-induced conformation. Virology. 171: 611-614. PMID 2548332 DOI: 10.1016/0042-6822(89)90632-6 |
0.317 |
|
| 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 |
0.413 |
|
| 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 |
0.428 |
|
| 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 |
0.505 |
|
| 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 |
0.428 |
|
| 1987 |
Arnold E, Vriend G, Luo M, Griffith JP, Kamer G, Erickson JW, Johnson JE, Rossmann MG. The structure determination of a common cold virus, human rhinovirus 14 Acta Crystallographica Section a Foundations of Crystallography. 43: 346-361. DOI: 10.1107/S0108767387099306 |
0.541 |
|
| 1987 |
Vriend G, Rossmann MG. Determination of the orientation of a randomly placed crystal from a single oscillation photograph Journal of Applied Crystallography. 20: 338-343. DOI: 10.1107/S0021889887086515 |
0.354 |
|
| 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 |
0.525 |
|
| 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 DOI: 10.1126/Science.3018924 |
0.375 |
|
| 1986 |
Rossmann MG, Arnold E, Vriend G. Comparison of vector search and feedback methods for finding heavy-atom sites in isomorphous derivatives Acta Crystallographica Section a Foundations of Crystallography. 42: 325-334. DOI: 10.1107/S0108767386099178 |
0.382 |
|
| 1986 |
Vriend G, Rossmann MG, Arnold E, Luo M, Griffith JP, Moffat K. Post-refinement of oscillation diffraction data collected at a synchrotron radiation source Journal of Applied Crystallography. 19: 134-139. DOI: 10.1107/S0021889886089793 |
0.353 |
|
| 1985 |
Vriend G, Hemminga MA, Haasnoot CAG, Hilbers CW. A two-dimensional nuclear overhauser enhancement NMR spectroscopy study at 500 MHz on cowpea chlorotic mottle virus protein assembled in spherical capsids Journal of Magnetic Resonance (1969). 64: 501-505. DOI: 10.1016/0022-2364(85)90113-1 |
0.499 |
|
| 1984 |
Arnold E, Ericksson JW, Frankenberger EA, Hecht H, Luo M, Rossmann MG, Vriend G. Progress in the structure determination of a common cold virus Acta Crystallographica Section a Foundations of Crystallography. 40: C48-C48. DOI: 10.1107/S0108767384098317 |
0.402 |
|
| 1984 |
Vriend G, Schilthuis JG, Verduin BJM, Hemminga MA. Saturation-transfer ESR spectroscopy on maleimide spin-labeled cowpea chlorotic mottle virus Journal of Magnetic Resonance (1969). 58: 421-427. DOI: 10.1016/0022-2364(84)90146-X |
0.433 |
|
| 1982 |
Vriend G, Verduin BJM, Hemminga MA, Schaafsma TJ. Mobility involved in protein-RNA interaction in spherical plant viruses, studied by nuclear magnetic resonance spectroscopy Febs Letters. 145: 49-52. DOI: 10.1016/0014-5793(82)81204-0 |
0.646 |
|
| 1982 |
Vriend G, Hemminga MA, Verduin BJM, Schaafsma TJ. Swelling of cowpea chlorotic mottle virus studied by proton nuclear magnetic resonance Febs Letters. 146: 319-321. DOI: 10.1016/0014-5793(82)80943-5 |
0.631 |
|
| 1981 |
Vriend G, Hemminga MA, Verduin BJM, Wit JLD, Schaafsma TJ. Segmental mobility involved in protein-RNA interaction in cowpea chlorotic mottle virus Febs Letters. 134: 167-171. DOI: 10.1016/0014-5793(81)80593-5 |
0.648 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 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 DOI: 10.1093/Protein/Gzg105 |
0.3 |
|
| 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 |
0.298 |
|
| 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 |
0.297 |
|
| 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 |
0.297 |
|
| 1996 |
Hooft RWW, Vriend G, Sander C, Abola EE. Errors in protein structures [3] Nature. 381: 272. PMID 8692262 DOI: 10.1038/381272A0 |
0.296 |
|
| 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 |
0.295 |
|
| 1993 |
Cronet P, Sander C, Vriend G. Modeling of transmembrane seven helix bundles Protein Engineering. 6: 59-64. PMID 8381957 DOI: 10.1093/Protein/6.1.59 |
0.295 |
|
| 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 |
0.294 |
|
| 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 |
0.292 |
|
| 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 |
0.291 |
|
| 2013 |
Aerts D, Verhaeghe T, Joosten HJ, Vriend G, Soetaert W, Desmet T. Consensus engineering of sucrose phosphorylase: the outcome reflects the sequence input. Biotechnology and Bioengineering. 110: 2563-72. PMID 23613221 DOI: 10.1002/Bit.24940 |
0.29 |
|
| 2016 |
Touw WG, van Beusekom B, Evers JM, Vriend G, Joosten RP. Validation and correction of Zn-CysxHisy complexes. Acta Crystallographica. Section D, Structural Biology. 72: 1110-1118. PMID 27710932 DOI: 10.1107/S2059798316013036 |
0.288 |
|
| 2006 |
Ott MA, Vriend G. Correcting ligands, metabolites, and pathways. Bmc Bioinformatics. 7: 517. PMID 17132165 DOI: 10.1186/1471-2105-7-517 |
0.288 |
|
| 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 |
0.287 |
|
| 2015 |
Touw WG, Joosten RP, Vriend G. Detection oftrans–cisflips and peptide plane flips in protein structures Acta Crystallographica Section a Foundations and Advances. 71: s270-s270. DOI: 10.1107/S2053273315095881 |
0.287 |
|
| 2010 |
Touw WG, Vriend G. On the complexity of Engh and Huber refinement restraints: the angle τ as example. Acta Crystallographica. Section D, Biological Crystallography. 66: 1341-50. PMID 21123875 DOI: 10.1107/S0907444910040928 |
0.286 |
|
| 1990 |
Vriend G. WHAT IF: a molecular modeling and drug design program. Journal of Molecular Graphics. 8: 52-6, 29. PMID 2268628 DOI: 10.1016/0263-7855(90)80070-V |
0.286 |
|
| 2012 |
Lounnas V, Vriend G. AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles. Journal of Chemical Information and Modeling. 52: 568-76. PMID 22299625 DOI: 10.1021/Ci2004303 |
0.286 |
|
| 2008 |
Ye K, Vriend G, IJzerman AP. Tracing evolutionary pressure. Bioinformatics (Oxford, England). 24: 908-15. PMID 18304936 DOI: 10.1093/Bioinformatics/Btn057 |
0.285 |
|
| 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 |
0.283 |
|
| 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 |
0.283 |
|
| 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 |
0.282 |
|
| 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 |
0.281 |
|
| 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 |
0.279 |
|
| 2012 |
Lütteke T, Mokros D, Joosten RP, Dominik A, Vriend G. New features and improvements in carbohydrate three-dimensional structure validation Acta Crystallographica Section a Foundations of Crystallography. 68: s22-s22. DOI: 10.1107/S0108767312099576 |
0.274 |
|
| 1994 |
Lakey JH, Parker MW, González-Mañas JM, Duché D, Vriend G, Baty D, Pattus F. The role of electrostatic charge in the membrane insertion of colicin A. Calculation and mutation. European Journal of Biochemistry / Febs. 220: 155-63. PMID 8119283 DOI: 10.1111/J.1432-1033.1994.Tb18610.X |
0.273 |
|
| 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: e41023. PMID 22848423 DOI: 10.1371/Journal.Pone.0041023 |
0.271 |
|
| 2013 |
Kim HJ, Won HH, Park KJ, Hong SH, Ki CS, Cho SS, Venselaar H, Vriend G, Kim JW. SNP linkage analysis and whole exome sequencing identify a novel POU4F3 mutation in autosomal dominant late-onset nonsyndromic hearing loss (DFNA15). Plos One. 8: e79063. PMID 24260153 DOI: 10.1371/Journal.Pone.0079063 |
0.268 |
|
| 2015 |
Touw WG, Joosten RP, Vriend G. Detection of trans-cis flips and peptide-plane flips in protein structures. Acta Crystallographica. Section D, Biological Crystallography. 71: 1604-14. PMID 26249342 DOI: 10.1107/S1399004715008263 |
0.266 |
|
| 2017 |
Wiel L, Venselaar H, Veltman JA, Vriend G, Gilissen C. Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics. Human Mutation. PMID 28815929 DOI: 10.1002/Humu.23313 |
0.265 |
|
| 2012 |
Vroling B, Thorne D, McDermott P, Joosten HJ, Attwood TK, Pettifer S, Vriend G. NucleaRDB: information system for nuclear receptors. Nucleic Acids Research. 40: D377-80. PMID 22064856 DOI: 10.1093/Nar/Gkr960 |
0.265 |
|
| 2014 |
Touw WG, Vriend G. BDB: databank of PDB files with consistent B-factors. Protein Engineering, Design & Selection : Peds. 27: 457-62. PMID 25336027 DOI: 10.1093/Protein/Gzu044 |
0.265 |
|
| 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 |
0.265 |
|
| 2016 |
Khandelwal KD, Ishorst N, Zhou H, Ludwig KU, Venselaar H, Gilissen C, Thonissen M, van Rooij IA, Dreesen K, Steehouwer M, van de Vorst M, Bloemen M, van Beusekom E, Roosenboom J, Borstlap W, ... ... Vriend G, et al. Novel IRF6 Mutations Detected in Orofacial Cleft Patients by Targeted Massively Parallel Sequencing. Journal of Dental Research. PMID 27834299 DOI: 10.1177/0022034516678829 |
0.264 |
|
| 2004 |
Vriend G. Protein design: quo vadis? Science (New York, N.Y.). 306: 1135. PMID 15539588 DOI: 10.1126/Science.306.5699.1135A |
0.264 |
|
| 2008 |
Lutteke T, Joosten R, Vriend G. Validation and correction of carbohydrate 3D structures Acta Crystallographica Section a Foundations of Crystallography. 64: C220-C221. DOI: 10.1107/S010876730809291X |
0.263 |
|
| 2017 |
Schaftenaar G, Vlieg E, Vriend G. Molden 2.0: quantum chemistry meets proteins. Journal of Computer-Aided Molecular Design. PMID 28752344 DOI: 10.1007/S10822-017-0042-5 |
0.262 |
|
| 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. PMID 21910883 DOI: 10.1186/1471-2105-12-362 |
0.261 |
|
| 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 |
0.259 |
|
| 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 |
0.255 |
|
| 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 |
0.254 |
|
| 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. Journal of Computer-Aided Molecular Design. 26: 137-50. PMID 22252446 DOI: 10.1007/S10822-011-9519-9 |
0.252 |
|
| 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 |
0.25 |
|
| 2012 |
Kopfer DA, Hahn U, Ohmert I, Vriend G, Pongs O, de Groot BL, Zachariae U. Molecular Determinants in K+ Channel hERG Inactivation Gating Biophysical Journal. 102: 529a-530a. DOI: 10.1016/J.Bpj.2011.11.2894 |
0.25 |
|
| 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 |
0.249 |
|
| 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, et al. Dominant missense mutations in ABCC9 cause Cantú syndrome. Nature Genetics. 44: 793-6. PMID 22610116 DOI: 10.1038/Ng.2324 |
0.249 |
|
| 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 |
0.249 |
|
| 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 |
0.245 |
|
| 2014 |
Lounnas V, Wedler HB, Newman T, Schaftenaar G, Harrison JG, Nepomuceno G, Pemberton R, Tantillo DJ, Vriend G. Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol. Journal of Computer-Aided Molecular Design. 28: 1057-67. PMID 25091066 DOI: 10.1007/S10822-014-9782-7 |
0.245 |
|
| 2002 |
Krieger E, Vriend G. Models@Home: distributed computing in bioinformatics using a screensaver based approach. Bioinformatics (Oxford, England). 18: 315-8. PMID 11847079 DOI: 10.1093/Bioinformatics/18.2.315 |
0.244 |
|
| 1990 |
Vriend G. Parameter relation rows: a query system for protein structure function relationships. Protein Engineering. 4: 221-3. PMID 2075196 DOI: 10.1093/protein/4.2.221 |
0.244 |
|
| 2015 |
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, ... ... Vriend G, et al. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research. PMID 26538599 DOI: 10.1093/Nar/Gkv1116 |
0.243 |
|
| 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 |
0.243 |
|
| 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 DOI: 10.1093/Protein/7.1.23 |
0.242 |
|
| 1991 |
Eijsink VG, van der Zee JR, van den Burg B, Vriend G, Venema G. Improving the thermostability of the neutral protease of Bacillus stearothermophilus by replacing a buried asparagine by leucine. Febs Letters. 282: 13-6. PMID 2026247 DOI: 10.1016/0014-5793(91)80434-5 |
0.241 |
|
| 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 |
0.241 |
|
| 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 |
0.241 |
|
| 2012 |
Gisel A, Attwood T, Helden Jv, Valverde JR, Conesa A, Herwig R, Korpelainen E, Mäkinen V, Pettifer S, Policriti A, Svensson T, Vriend G, Bongcam-Rudloff E. COST Action BM 1006 (SeqAhead): MC BUSINESS MEETING AND SCIENTIFIC MEETING Embnet.Journal. 17: 4-7. DOI: 10.14806/Ej.17.B.297 |
0.239 |
|
| 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 |
0.239 |
|
| 2015 |
Oh SK, Baek JI, Weigand KM, Venselaar H, Swarts HG, Park SH, Hashim Raza M, Jung da J, Choi SY, Lee SH, Friedrich T, Vriend G, Koenderink JB, Kim UK, Lee KY. A missense variant of the ATP1A2 gene is associated with a novel phenotype of progressive sensorineural hearing loss associated with migraine. European Journal of Human Genetics : Ejhg. 23: 639-45. PMID 25138102 DOI: 10.1038/Ejhg.2014.154 |
0.237 |
|
| 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, et al. Human dectin-1 deficiency and mucocutaneous fungal infections. The New England Journal of Medicine. 361: 1760-7. PMID 19864674 DOI: 10.1056/Nejmoa0901053 |
0.236 |
|
| 2021 |
Bibbe JM, Vriend G. Motions around conserved helical weak spots facilitate GPCR activation. Proteins. PMID 34272892 DOI: 10.1002/prot.26179 |
0.231 |
|
| 2015 |
Touw W, Vriend G. Cis-trans flips: peptide bond conformation correction F1000research. 6. DOI: 10.7490/F1000Research.1097502.1 |
0.231 |
|
| 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 |
0.229 |
|
| 2016 |
Homberg JR, Olivier JD, VandenBroeke M, Youn J, Ellenbroek AK, Karel P, Shan L, van Boxtel R, Ooms S, Balemans M, Langedijk J, Muller M, Vriend G, Cools AR, Cuppen E, et al. The role of the dopamine D1 receptor in social cognition: studies using a novel genetic rat model. Disease Models & Mechanisms. PMID 27483345 DOI: 10.1242/Dmm.024752 |
0.229 |
|
| 1994 |
De Filippis V, Sander C, Vriend G. Predicting local structural changes that result from point mutations Protein Engineering. 7: 1203-1208. PMID 7855135 |
0.227 |
|
| 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 |
0.226 |
|
| 2019 |
Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, ... ... Vriend G, et al. The bio.tools registry of software tools and data resources for the life sciences. Genome Biology. 20: 164. PMID 31405382 DOI: 10.1186/S13059-019-1772-6 |
0.226 |
|
| 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 |
0.226 |
|
| 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 |
0.224 |
|
| 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 |
0.223 |
|
| 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 |
0.223 |
|
| 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, et al. Mutations in SMAD3 cause a syndromic form of aortic aneurysms and dissections with early-onset osteoarthritis. Nature Genetics. 43: 121-6. PMID 21217753 DOI: 10.1038/Ng.744 |
0.22 |
|
| 2015 |
Isberg V, de Graaf C, Bortolato A, Cherezov V, Katritch V, Marshall FH, Mordalski S, Pin JP, Stevens RC, Vriend G, Gloriam DE. Generic GPCR residue numbers - aligning topology maps while minding the gaps. Trends in Pharmacological Sciences. 36: 22-31. PMID 25541108 DOI: 10.1016/J.Tips.2014.11.001 |
0.219 |
|
| 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 (Oxford, England). 25: 2090-1. PMID 19460889 DOI: 10.1093/Bioinformatics/Btp329 |
0.217 |
|
| 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 |
0.215 |
|
| 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 |
0.215 |
|
| 1992 |
Vriend G, Sander C. Detection of common three-dimensional substructures in proteins. Proteins. 11: 52-8. PMID 1660134 DOI: 10.1002/Prot.340110107 |
0.214 |
|
| 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 |
0.213 |
|
| 2021 |
Poelman H, Ippel H, Gürkan B, Boelens R, Vriend G, Veer CV', Lutgens E, Nicolaes GAF. Structural anomalies in a published NMR-derived structure of IRAK-M. Journal of Molecular Graphics & Modelling. 111: 108061. PMID 34837785 DOI: 10.1016/j.jmgm.2021.108061 |
0.211 |
|
| 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 |
0.21 |
|
| 2015 |
Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G. A series of PDB-related databanks for everyday needs. Nucleic Acids Research. 43: D364-8. PMID 25352545 DOI: 10.1093/nar/gku1028 |
0.209 |
|
| 2010 |
Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, ... ... Vriend G, et al. The EMBRACE web service collection. Nucleic Acids Research. 38: W683-8. PMID 20462862 DOI: 10.1093/Nar/Gkq297 |
0.207 |
|
| 2014 |
Isberg V, Vroling B, van der Kant R, Li K, Vriend G, Gloriam D. GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Research. 42: D422-5. PMID 24304901 DOI: 10.1093/nar/gkt1255 |
0.206 |
|
| 1991 |
Eijsink VG, Vriend G, Van Den Burg B, Venema G, Stulp BK. Contribution of the C-terminal amino acid to the stability of Bacillus subtilis neutral protease. Protein Engineering. 4: 99-104. PMID 2127107 DOI: 10.1093/Protein/4.1.99 |
0.206 |
|
| 2015 |
Wedler HB, Pemberton RP, Lounnas V, Vriend G, Tantillo DJ, Wang SC. Quantum chemical study of the isomerization of 24-methylenecycloartanol, a potential marker of olive oil refining. Journal of Molecular Modeling. 21: 111. PMID 25860110 DOI: 10.1007/S00894-015-2652-Y |
0.206 |
|
| 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 |
0.205 |
|
| 1982 |
Akeroyd R, Lenstra JA, Westerman J, Vriend G, Wirtz KW, van Deenen LL. Prediction of secondary structural elements in the phosphatidylcholine-transfer protein from bovine liver. European Journal of Biochemistry / Febs. 121: 391-4. PMID 7060554 DOI: 10.1111/J.1432-1033.1982.Tb05799.X |
0.205 |
|
| 2015 |
Isberg V, Mordalski S, Munk C, Rataj K, Harpsøe K, Hauser AS, Vroling B, Bojarski AJ, Vriend G, Gloriam DE. GPCRdb: an information system for G protein-coupled receptors. Nucleic Acids Research. PMID 26582914 DOI: 10.1093/nar/gkv1178 |
0.205 |
|
| 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 |
0.203 |
|
| 1996 |
Hooft RWW, Sander C, Vriend G. Verification of Protein Structures: Side-Chain Planarity Journal of Applied Crystallography. 29: 714-716. |
0.203 |
|
| 2017 |
Vollan HS, Tannæs T, Caugant DA, Vriend G, Bukholm G. Outer membrane phospholipase A's roles in Helicobacter pylori acid adaptation. Gut Pathogens. 9: 36. PMID 28616083 DOI: 10.1186/S13099-017-0184-Y |
0.202 |
|
| 2018 |
Seijkens TTP, van Tiel CM, Kusters PJH, Atzler D, Soehnlein O, Zarzycka B, Aarts SABM, Lameijer M, Gijbels MJ, Beckers L, den Toom M, Slütter B, Kuiper J, Duchene J, Aslani M, ... ... Vriend G, et al. Targeting CD40-Induced TRAF6 Signaling in Macrophages Reduces Atherosclerosis. Journal of the American College of Cardiology. 71: 527-542. PMID 29406859 DOI: 10.1016/J.Jacc.2017.11.055 |
0.202 |
|
| 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 DOI: 10.1093/Bioinformatics/13.4.425 |
0.201 |
|
| 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 |
0.2 |
|
| 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 |
0.197 |
|
| 2011 |
Vroling B, Sanders M, Baakman C, Borrmann A, Verhoeven S, Klomp J, Oliveira L, de Vlieg J, Vriend G. GPCRDB: information system for G protein-coupled receptors. Nucleic Acids Research. 39: D309-19. PMID 21045054 DOI: 10.1093/nar/gkq1009 |
0.196 |
|
| 2020 |
Rademaker D, van Dijk J, Titulaer W, Lange J, Vriend G, Xue L. The Future of Protein Secondary Structure Prediction Was Invented by Oleg Ptitsyn. Biomolecules. 10. PMID 32560074 DOI: 10.3390/biom10060910 |
0.195 |
|
| 2014 |
Chatzigeorgiou A, Seijkens T, Zarzycka B, Engel D, Poggi M, van den Berg S, van den Berg S, Soehnlein O, Winkels H, Beckers L, Lievens D, Driessen A, Kusters P, Biessen E, Garcia-Martin R, ... ... Vriend G, et al. Blocking CD40-TRAF6 signaling is a therapeutic target in obesity-associated insulin resistance. Proceedings of the National Academy of Sciences of the United States of America. 111: 2686-91. PMID 24492375 DOI: 10.1073/Pnas.1400419111 |
0.195 |
|
| 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 |
0.194 |
|
| 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 |
0.193 |
|
| 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 |
0.19 |
|
| 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 |
0.189 |
|
| 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 |
0.185 |
|
| 2017 |
McGuire R, Verhoeven S, Vass M, Vriend G, De Esch IJ, Lusher SJ, Leurs R, Ridder L, Kooistra AJ, Ritschel T, de Graaf C. 3D-e-Chem-VM: Structural cheminformatics research infrastructure in a freely available Virtual Machine. Journal of Chemical Information and Modeling. PMID 28125221 DOI: 10.1021/acs.jcim.6b00686 |
0.184 |
|
| 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 |
0.183 |
|
| 2014 |
Chatzigeorgiou A, Seijkens T, Zarzycka B, Engel D, Poggi M, Van Den Berg S, Soehnlein O, Winkels H, Beckers L, Lievens D, Driessen A, Kusters P, Biessen E, Garcia-Martin R, Ameln AKV, ... ... Vriend G, et al. Blocking CD40-TRAF6 signaling is a therapeutic target in obesity-associated insulin resistance (Proceedings of the National Academy of Sciences of the United States of America (2014) 111, 7 (2686-2691) DOI: 10.1073/pnas.1400419111) Proceedings of the National Academy of Sciences of the United States of America. 111: 4644. DOI: 10.1073/Pnas.1403231111 |
0.182 |
|
| 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 |
0.18 |
|
| 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 |
0.178 |
|
| 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 |
0.177 |
|
| 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 |
0.175 |
|
| 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 |
0.174 |
|
| 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 |
0.174 |
|
| 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 |
0.169 |
|
| 1990 |
Eggink G, Engel H, Vriend G, Terpstra P, Witholt B. Rubredoxin reductase of Pseudomonas oleovorans. Structural relationship to other flavoprotein oxidoreductases based on one NAD and two FAD fingerprints. Journal of Molecular Biology. 212: 135-42. PMID 2319593 DOI: 10.1016/0022-2836(90)90310-I |
0.167 |
|
| 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 |
0.161 |
|
| 2019 |
Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Human Mutation. 40: 1030-1038. PMID 31116477 DOI: 10.1002/humu.23798 |
0.159 |
|
| 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 |
0.158 |
|
| 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 DOI: 10.1093/Protein/14.11.897 |
0.158 |
|
| 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 |
0.157 |
|
| 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 |
0.157 |
|
| 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 |
0.157 |
|
| 2022 |
Rademaker DT, Xue LC, 't Hoen PAC, Vriend G. Entropy and Variability: A Second Opinion by Deep Learning. Biomolecules. 12. PMID 36551168 DOI: 10.3390/biom12121740 |
0.154 |
|
| 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 |
0.152 |
|
| 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 |
0.152 |
|
| 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 |
0.151 |
|
| 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 |
0.151 |
|
| 2012 |
Wassenaar TA, van Dijk M, Loureiro-Ferreira N, van der Schot G, de Vries SJ, Schmitz C, van der Zwan J, Boelens R, Giachetti A, Ferella L, Rosato A, Bertini I, Herrmann T, Jonker HRA, Bagaria A, ... ... Vriend G, et al. WeNMR: Structural Biology on the Grid Journal of Grid Computing. 10: 743-767. DOI: 10.1007/s10723-012-9246-z |
0.15 |
|
| 1979 |
Wirtz KW, Vriend G, Westerman J. Kinetic analysis of the interaction of the phosphatidylcholine exchange protein with unilamellar vesicels and multilamellar liposomes. European Journal of Biochemistry. 94: 215-21. PMID 35349 DOI: 10.1111/J.1432-1033.1979.Tb12888.X |
0.15 |
|
| 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 |
0.146 |
|
| 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. PMID 17537266 DOI: 10.1186/1471-2105-8-177 |
0.145 |
|
| 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 |
0.145 |
|
| 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 |
0.144 |
|
| 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 |
0.144 |
|
| 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 |
0.144 |
|
| 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 |
0.144 |
|
| 2015 |
Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, ... ... Vriend G, et al. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database : the Journal of Biological Databases and Curation. 2015: bav063. PMID 26284514 DOI: 10.1093/Database/Bav063 |
0.139 |
|
| 2017 |
Khandelwal KD, Ockeloen CW, Venselaar H, Boulanger C, Brichard B, Sokal E, Pfundt R, Rinne T, van Beusekom E, Bloemen M, Vriend G, Revencu N, Carels CEL, van Bokhoven H, Zhou H. Identification of a de novo variant in CHUK in a patient with an EEC/AEC syndrome-like phenotype and hypogammaglobulinemia. American Journal of Medical Genetics. Part A. PMID 28513979 DOI: 10.1002/ajmg.a.38274 |
0.137 |
|
| 2017 |
Lelieveld SH, Wiel L, Venselaar H, Pfundt R, Vriend G, Veltman JA, Brunner HG, Vissers LELM, Gilissen C. Spatial Clustering of de Novo Missense Mutations Identifies Candidate Neurodevelopmental Disorder-Associated Genes. American Journal of Human Genetics. PMID 28867141 DOI: 10.1016/j.ajhg.2017.08.004 |
0.136 |
|
| 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 |
0.133 |
|
| 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 |
0.132 |
|
| 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 |
0.126 |
|
| 2006 |
Paiva AC, Oliveira L, Horn F, Bywater RP, Vriend G. Modeling GPCRs. Ernst Schering Foundation Symposium Proceedings. 23-47. PMID 17703576 |
0.122 |
|
| 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 |
0.11 |
|
| 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 |
0.11 |
|
| 2016 |
Isberg V, Mordalski S, Munk C, Rataj K, Harpsøe K, Hauser AS, Vroling B, Bojarski AJ, Vriend G, Gloriam DE. GPCRdb: an information system for G protein-coupled receptors. Nucleic Acids Research. PMID 27923934 DOI: 10.1093/nar/gkw1218 |
0.108 |
|
| 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 |
0.108 |
|
| 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. |
0.106 |
|
| 1998 |
Horn F, Vriend G. G protein-coupled receptors in silico Journal of Molecular Medicine. 76: 464-468. PMID 9660164 DOI: 10.1007/s001090050240 |
0.105 |
|
| 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 |
0.102 |
|
| 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 |
0.1 |
|
| 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 |
0.099 |
|
| 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 |
0.098 |
|
| 1997 |
Van Burg Rung B, Eijsink V, Vriend G, Veltman R, Venema G. Manipulating bacillus neutral protease autolysis Protein Engineering. 10: 37. |
0.098 |
|
| 1987 |
Rossmann MC, Vriend G, Luo M, Arnold E, Kamer G, Smith TJ. Processing oscillation photographs of virus crystal diffracation data using the 'American method' Acta Crystallographica Section a Foundations of Crystallography. 43: C7-C7. DOI: 10.1107/S0108767387085349 |
0.097 |
|
| 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 |
0.092 |
|
| 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. |
0.091 |
|
| 2010 |
Schobers L, Venselaar H, Vriend G, Van Hest JCM. Synthesis of covalently linked enzyme dimers sanne schoffelen1 Acs Symposium Series. 1043: 125-139. DOI: 10.1021/bk-2010-1043.ch010 |
0.089 |
|
| 2003 |
Krieger E, Nabuurs SB, Vriend G. Homology modeling. Methods of Biochemical Analysis. 44: 509-23. PMID 12647402 |
0.083 |
|
| 2015 |
Micha D, Guo DC, Hilhorst-Hofstee Y, van Kooten F, Atmaja D, Overwater E, Cayami FK, Regalado ES, van Uffelen R, Venselaar H, Faradz SM, Vriend G, Weiss MM, Sistermans EA, Maugeri A, et al. SMAD2 Mutations Are Associated with Arterial Aneurysms and Dissections. Human Mutation. PMID 26247899 DOI: 10.1002/Humu.22854 |
0.081 |
|
| 2014 |
Schwarte A, Venselaar H, Haase P, Vriend G. The newprot self-service portal for protein engineering Ceur Workshop Proceedings. 1320. |
0.075 |
|
| 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 |
0.074 |
|
| 2010 |
Vroling B, Bywater RP, Oliveira L, Vriend G. GPCRs: Past, present, and future Structural Bioinformatics of Membrane Proteins. 251-278. DOI: 10.1007/978-3-7091-0045-5_14 |
0.061 |
|
| 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. |
0.055 |
|
| 2023 |
Rademaker DT, Koopmans JJ, Thyen GMSM, Piruska A, Huck WTS, Vriend G, 't Hoen PAC, Kooij TWA, Huynen MA, Proellochs NI. Quantifying the deformability of malaria-infected red blood cells using deep learning trained on synthetic cells. Iscience. 26: 108542. PMID 38089575 DOI: 10.1016/j.isci.2023.108542 |
0.047 |
|
| 2013 |
Ronchieri E, Verlato M, Salomoni D, Dalla Torre G, Italiano A, Ciaschini V, Andreotti D, Dal Pra S, Touw WG, Vriend G, Vuister GW. Accessing scientific applications through the wnodes cloud virtualization framework Proceedings of Science. |
0.037 |
|
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