Sequence comparison by sequence harmony identifies subtype-specific functional sites

door Pirovano, Walter, Feenstra, K. Anton, Heringa, Jaap
Gepubliceerd in 2006

The meaning of alignment: lessons from structural diversity

door Pirovano, Walter, Feenstra, K Anton, Heringa, Jaap
Gepubliceerd in 2008

Multi-Harmony: detecting functional specificity from sequence alignment

door Brandt, Bernd W., Feenstra, K. Anton, Heringa, Jaap
Gepubliceerd in 2010

Sequence harmony: detecting functional specificity from alignments

door Feenstra, K. Anton, Pirovano, Walter, Krab, Klaas, Heringa, Jaap
Gepubliceerd in 2007

CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys

door Hou, Qingzhen, Lensink, Marc F., Heringa, Jaap, Feenstra, K. Anton
Gepubliceerd in PLoS One (2016)

Structure and function analysis of flexible alignment regions in proteins

door Pirovano, Walter, Reijden, Anneke van der, Feenstra, K Anton, Heringa, Jaap
Gepubliceerd in 2009

Sequence specificity between interacting and non-interacting homologs identifies interface residues – a homodimer and monomer use case

door Hou, Qingzhen, Dutilh, Bas E., Huynen, Martijn A., Heringa, Jaap, Feenstra, K. Anton
Gepubliceerd in BMC Bioinformatics (2015)

BioASF: a framework for automatically generating executable pathway models specified in BioPAX

door Haydarlou, Reza, Jacobsen, Annika, Bonzanni, Nicola, Feenstra, K. Anton, Abeln, Sanne, Heringa, Jaap
Gepubliceerd in Bioinformatics (2016)

Motif-Aware PRALINE: Improving the alignment of motif regions

door Dijkstra, Maurits, Bawono, Punto, Abeln, Sanne, Feenstra, K. Anton, Fokkink, Wan, Heringa, Jaap
Gepubliceerd in PLoS Comput Biol (2018)

Predicting the relationships between gut microbiota and mental disorders with knowledge graphs

door Liu, Ting, Pan, Xueli, Wang, Xu, Feenstra, K. Anton, Heringa, Jaap, Huang, Zhisheng
Gepubliceerd in Health Inf Sci Syst (2020)

Online biophysical predictions for SARS-CoV-2 proteins

door Kagami, Luciano, Roca-Martínez, Joel, Gavaldá-García, Jose, Ramasamy, Pathmanaban, Feenstra, K. Anton, Vranken, Wim F.
Gepubliceerd in BMC Mol Cell Biol (2021)

Enantioselective Substrate Binding in a Monooxygenase Protein Model by Molecular Dynamics and Docking

door Feenstra, K. Anton, Hofstetter, Karin, Bosch, Rolien, Schmid, Andreas, Commandeur, Jan N. M., Vermeulen, Nico P. E.
Gepubliceerd in 2006

Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants

door Feenstra, K. Anton, Starikov, Eugene B., Urlacher, Vlada B., Commandeur, Jan N.M., Vermeulen, Nico P.E.
Gepubliceerd in 2007

Construction and Experimental Validation of a Petri Net Model of Wnt/β-Catenin Signaling

door Jacobsen, Annika, Heijmans, Nika, Verkaar, Folkert, Smit, Martine J., Heringa, Jaap, van Amerongen, Renée, Feenstra, K. Anton
Gepubliceerd in PLoS One (2016)

HIV-1 Replication Fitness of HLA-B*57/58:01 CTL Escape Variants Is Restored by the Accumulation of Compensatory Mutations in Gag

door Gijsbers, Esther F., Feenstra, K. Anton, van Nuenen, Ad C., Navis, Marjon, Heringa, Jaap, Schuitemaker, Hanneke, Kootstra, Neeltje A.
Gepubliceerd in 2013

The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interact...

door Amini, Saman, Jacobsen, Annika, Ivanova, Olga, Lijnzaad, Philip, Heringa, Jaap, Holstege, Frank C. P., Feenstra, K. Anton, Kemmeren, Patrick
Gepubliceerd in PLoS Comput Biol (2019)

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit

door Dijkstra, Maurits J J, van der Ploeg, Atze J, Feenstra, K Anton, Fokkink, Wan J, Abeln, Sanne, Heringa, Jaap
Gepubliceerd in Bioinformatics (2019)

SeRenDIP-CE: sequence-based interface prediction for conformational epitopes

door Hou, Qingzhen, Stringer, Bas, Waury, Katharina, Capel, Henriette, Haydarlou, Reza, Xue, Fuzhong, Abeln, Sanne, Heringa, Jaap, Feenstra, K Anton
Gepubliceerd in Bioinformatics (2021)

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model

door Bonzanni, Nicola, Garg, Abhishek, Feenstra, K. Anton, Schütte, Judith, Kinston, Sarah, Miranda-Saavedra, Diego, Heringa, Jaap, Xenarios, Ioannis, Göttgens, Berthold
Gepubliceerd in 2013

HIV-1 envelope glycoprotein signatures that correlate with the development of cross-reactive neutralizing activity

door van den Kerkhof, Tom L G M, Feenstra, K Anton, Euler, Zelda, van Gils, Marit J, Rijsdijk, Linda W E, Boeser-Nunnink, Brigitte D, Heringa, Jaap, Schuitemaker, Hanneke, Sanders, Rogier W
Gepubliceerd in 2013