Herman W T van Vlijmen

Herman W T van Vlijmen

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Herman W T van Vlijmen

Herman W T van Vlijmen

Publications by authors named "Herman W T van Vlijmen"

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28Publications

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Advances and Challenges in Computational Target Prediction.

J Chem Inf Model 2019 May 28;59(5):1728-1742. Epub 2019 Feb 28.

In silico Toxicology, Institute of Physiology , Charité - Universitätsmedizin Berlin , Charitéplatz 1 , 10117 Berlin , Germany.

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http://dx.doi.org/10.1021/acs.jcim.8b00832DOI Listing
May 2019

An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A receptor.

J Cheminform 2019 May 24;11(1):35. Epub 2019 May 24.

Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands.

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http://dx.doi.org/10.1186/s13321-019-0355-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6534880PMC
May 2019

Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling.

J Cheminform 2019 Feb 14;11(1):15. Epub 2019 Feb 14.

Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.

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http://dx.doi.org/10.1186/s13321-019-0337-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6689890PMC
February 2019

Corrigendum to "Chemical space screening around Phe in opioid peptides: Modulating µ versus δ agonism by Suzuki-Miyaura cross-couplings" [Bioorg. Med. Chem. Lett. 28(13) (2018) 2320-2323].

Bioorg Med Chem Lett 2018 11 5;28(20):3418. Epub 2018 Sep 5.

Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. Electronic address:

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http://dx.doi.org/10.1016/j.bmcl.2018.08.023DOI Listing
November 2018

Chemical space screening around Phe in opioid peptides: Modulating µ versus δ agonism by Suzuki-Miyaura cross-couplings.

Bioorg Med Chem Lett 2018 07 12;28(13):2320-2323. Epub 2018 May 12.

Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. Electronic address:

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http://dx.doi.org/10.1016/j.bmcl.2018.05.015DOI Listing
July 2018

Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling.

J Chem Inf Model 2017 12 12;57(12):2976-2985. Epub 2017 Dec 12.

ChEMBL Group, EMBL-EBI, Wellcome Trust Genome Campus, CB10 1SD Hinxton, United Kingdom.

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http://dx.doi.org/10.1021/acs.jcim.7b00338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5755953PMC
December 2017

Blood-based metabolic signatures in Alzheimer's disease.

Alzheimers Dement (Amst) 2017 6;8:196-207. Epub 2017 Sep 6.

Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.dadm.2017.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607205PMC
September 2017

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set.

J Cheminform 2017 Aug 14;9(1):45. Epub 2017 Aug 14.

Division of Medicinal Chemistry, Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.

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http://dx.doi.org/10.1186/s13321-017-0232-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5555960PMC
August 2017

Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study.

J Chem Theory Comput 2017 Mar 3;13(3):1439-1453. Epub 2017 Feb 3.

Computational Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain.

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http://dx.doi.org/10.1021/acs.jctc.6b01141DOI Listing
March 2017

Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening.

J Chem Inf Model 2016 10 27;56(10):2053-2060. Epub 2016 Sep 27.

Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , 2333 CC Leiden, The Netherlands.

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http://dx.doi.org/10.1021/acs.jcim.6b00314DOI Listing
October 2016

In search of novel ligands using a structure-based approach: a case study on the adenosine A receptor.

J Comput Aided Mol Des 2016 10 15;30(10):863-874. Epub 2016 Sep 15.

Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.

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http://dx.doi.org/10.1007/s10822-016-9963-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5083784PMC
October 2016

Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor.

J Chem Inf Model 2014 Jun 3;54(6):1737-46. Epub 2014 Jun 3.

Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands.

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http://dx.doi.org/10.1021/ci5000455DOI Listing
June 2014

Influence of canonical structure determining residues on antibody affinity and stability.

J Struct Biol 2014 Feb 29;185(2):223-7. Epub 2013 Aug 29.

Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2013.08.009DOI Listing
February 2014

Antibody humanization by redesign of complementarity-determining region residues proximate to the acceptor framework.

Methods 2014 Jan 28;65(1):68-76. Epub 2013 Jun 28.

Biogen Idec, 12 Cambridge Center, Cambridge, MA 02142, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2013.06.024DOI Listing
January 2014

Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data.

J Med Chem 2012 Aug 3;55(16):7010-20. Epub 2012 Aug 3.

Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.

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http://dx.doi.org/10.1021/jm3003069DOI Listing
August 2012

Mining protein dynamics from sets of crystal structures using "consensus structures".

Protein Sci 2010 Apr;19(4):742-52

Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Einsteinweg 55, 2333 CC Leiden, Netherlands.

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http://doi.wiley.com/10.1002/pro.350
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http://dx.doi.org/10.1002/pro.350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867014PMC
April 2010

An antibody loop replacement design feasibility study and a loop-swapped dimer structure.

Protein Eng Des Sel 2009 Feb 10;22(2):93-101. Epub 2008 Dec 10.

Biogen Idec Inc., Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/protein/gzn072DOI Listing
February 2009

A knowledge-based forcefield for protein-protein interface design.

Proteins 2008 Mar;70(4):1540-50

Biogen Idec Inc., Protein Engineering Group, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1002/prot.21694DOI Listing
March 2008

Trends in antibody sequence changes during the somatic hypermutation process.

J Immunol 2006 Jul;177(1):333-40

Biogen Idec Inc., 14 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.4049/jimmunol.177.1.333DOI Listing
July 2006

Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry.

J Mol Biol 2005 Jul 7;350(3):528-42. Epub 2005 Apr 7.

Computational Drug Design Group, Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.jmb.2005.03.028DOI Listing
July 2005

A classification of disulfide patterns and its relationship to protein structure and function.

Protein Sci 2004 Aug;13(8):2045-58

Computational Drug Design Group, Biogen Idec, Inc., Cambridge, Masschusetts 02142, USA.

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http://doi.wiley.com/10.1110/ps.04613004
Publisher Site
http://dx.doi.org/10.1110/ps.04613004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279833PMC
August 2004

A novel database of disulfide patterns and its application to the discovery of distantly related homologs.

J Mol Biol 2004 Jan;335(4):1083-92

Structural Informatics Group, Biogen Inc., 14 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.jmb.2003.10.077DOI Listing
January 2004