Sequence comparison by sequence harmony identifies subtype-specific functional sites

od Pirovano, Walter, Feenstra, K. Anton, Heringa, Jaap
Wydane 2006

The meaning of alignment: lessons from structural diversity

od Pirovano, Walter, Feenstra, K Anton, Heringa, Jaap
Wydane 2008

Multi-Harmony: detecting functional specificity from sequence alignment

od Brandt, Bernd W., Feenstra, K. Anton, Heringa, Jaap
Wydane 2010

Sequence harmony: detecting functional specificity from alignments

od Feenstra, K. Anton, Pirovano, Walter, Krab, Klaas, Heringa, Jaap
Wydane 2007

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

od Hou, Qingzhen, Lensink, Marc F., Heringa, Jaap, Feenstra, K. Anton
Wydane w PLoS One (2016)

Structure and function analysis of flexible alignment regions in proteins

od Pirovano, Walter, Reijden, Anneke van der, Feenstra, K Anton, Heringa, Jaap
Wydane 2009

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

od Hou, Qingzhen, Dutilh, Bas E., Huynen, Martijn A., Heringa, Jaap, Feenstra, K. Anton
Wydane w BMC Bioinformatics (2015)

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

od Haydarlou, Reza, Jacobsen, Annika, Bonzanni, Nicola, Feenstra, K. Anton, Abeln, Sanne, Heringa, Jaap
Wydane w Bioinformatics (2016)

Motif-Aware PRALINE: Improving the alignment of motif regions

od Dijkstra, Maurits, Bawono, Punto, Abeln, Sanne, Feenstra, K. Anton, Fokkink, Wan, Heringa, Jaap
Wydane w PLoS Comput Biol (2018)

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

od Liu, Ting, Pan, Xueli, Wang, Xu, Feenstra, K. Anton, Heringa, Jaap, Huang, Zhisheng
Wydane w Health Inf Sci Syst (2020)

Online biophysical predictions for SARS-CoV-2 proteins

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

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

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

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

od Feenstra, K. Anton, Starikov, Eugene B., Urlacher, Vlada B., Commandeur, Jan N.M., Vermeulen, Nico P.E.
Wydane 2007

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

od Jacobsen, Annika, Heijmans, Nika, Verkaar, Folkert, Smit, Martine J., Heringa, Jaap, van Amerongen, Renée, Feenstra, K. Anton
Wydane w 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

od Gijsbers, Esther F., Feenstra, K. Anton, van Nuenen, Ad C., Navis, Marjon, Heringa, Jaap, Schuitemaker, Hanneke, Kootstra, Neeltje A.
Wydane 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...

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

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

od Dijkstra, Maurits J J, van der Ploeg, Atze J, Feenstra, K Anton, Fokkink, Wan J, Abeln, Sanne, Heringa, Jaap
Wydane w Bioinformatics (2019)

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

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

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

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

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

od 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
Wydane 2013