![](https://dblp.uni-trier.de/img/logo.320x120.png)
![search dblp search dblp](https://dblp.uni-trier.de/img/search.dark.16x16.png)
![search dblp](https://dblp.uni-trier.de/img/search.dark.16x16.png)
default search action
Alan E. Mark
Person information
SPARQL queries ![](https://dblp.uni-trier.de/img/new.blue.24x12.png)
Refine list
![note](https://dblp.uni-trier.de/img/note-mark.dark.12x12.png)
refinements active!
zoomed in on ?? of ?? records
view refined list in
export refined list as
2020 – today
- 2023
- [j22]Martin Stroet
, Bertrand Caron, Martin S. Engler
, Jimi van der Woning, Aude Kauffmann
, Marc van Dijk
, Mohammed El-Kebir
, Koen Visscher, Josef Holownia
, Callum Macfarlane
, Brian J. Bennion
, Svetlana Gelpi-Dominguez
, Felice C. Lightstone
, Tijs van der Storm
, Daan P. Geerke
, Alan E. Mark
, Gunnar W. Klau
:
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. J. Comput. Aided Mol. Des. 37(8): 357-371 (2023) - [j21]Martin Stroet
, Stephen Sanderson
, Audrey V. Sanzogni, Sharif Nada
, Thomas Lee
, Bertrand Caron, Alan E. Mark
, Paul L. Burn
:
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies. J. Chem. Inf. Model. 63(1): 2-8 (2023)
2010 – 2019
- 2019
- [j20]Martin S. Engler
, Bertrand Caron, Lourens E. Veen, Daan P. Geerke
, Alan E. Mark
, Gunnar W. Klau
:
Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach. Algorithms Mol. Biol. 14(1): 1:1-1:10 (2019) - [j19]Nandhitha Subramanian
, Alexandra Schumann-Gillett
, Alan E. Mark
, Megan L. O'Mara
:
Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations. J. Chem. Inf. Model. 59(5): 2287-2298 (2019) - 2018
- [j18]Julian Zaugg
, Yosephine Gumulya
, Mikael Bodén
, Alan E. Mark
, Alpeshkumar K. Malde
:
Effect of Binding on Enantioselectivity of Epoxide Hydrolase. J. Chem. Inf. Model. 58(3): 630-640 (2018) - [c2]Martin S. Engler
, Bertrand Caron, Lourens E. Veen, Daan P. Geerke
, Alan E. Mark
, Gunnar W. Klau:
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules. WABI 2018: 16:1-16:13 - 2016
- [j17]Evelyne Deplazes
, Josephine Davies, Alexandre M. J. J. Bonvin
, Glenn F. King
, Alan E. Mark
:
Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a. J. Chem. Inf. Model. 56(1): 127-138 (2016) - 2015
- [j16]Nandhitha Subramanian
, Karmen Condic-Jurkic
, Alan E. Mark
, Megan L. O'Mara
:
Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques. J. Chem. Inf. Model. 55(6): 1202-1217 (2015) - 2014
- [j15]Katarzyna B. Koziara, Martin Stroet
, Alpeshkumar K. Malde
, Alan E. Mark
:
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. J. Comput. Aided Mol. Des. 28(3): 221-233 (2014) - 2013
- [j14]Stefan Canzar
, Mohammed El-Kebir
, René Pool
, Khaled M. Elbassioni
, Alan E. Mark
, Daan P. Geerke
, Leen Stougie, Gunnar W. Klau
:
Charge Group Partitioning in Biomolecular Simulation. J. Comput. Biol. 20(3): 188-198 (2013) - 2012
- [c1]Stefan Canzar
, Mohammed El-Kebir
, René Pool
, Khaled M. Elbassioni
, Alpeshkumar K. Malde
, Alan E. Mark, Daan P. Geerke
, Leen Stougie, Gunnar W. Klau
:
Charge Group Partitioning in Biomolecular Simulation. RECOMB 2012: 29-43 - 2011
- [j13]Alpeshkumar K. Malde
, Alan E. Mark
:
Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. J. Comput. Aided Mol. Des. 25(1): 1-12 (2011) - 2010
- [j12]David Poger
, Wilfred F. van Gunsteren, Alan E. Mark
:
A new force field for simulating phosphatidylcholine bilayers. J. Comput. Chem. 31(6): 1117-1125 (2010) - [j11]Clara D. Christ, Alan E. Mark
, Wilfred F. van Gunsteren:
Basic ingredients of free energy calculations: A review. J. Comput. Chem. 31(8): 1569-1582 (2010)
2000 – 2009
- 2009
- [j10]Xavier Periole
, Lucy R. Allen, Kamil Tamiola, Alan E. Mark
, Emanuele Paci
:
Probing the free energy landscape of the FBP28WW domain using multiple techniques. J. Comput. Chem. 30(7): 1059-1068 (2009) - 2006
- [j9]Tsjerk A. Wassenaar
, Alan E. Mark
:
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. J. Comput. Chem. 27(3): 316-325 (2006) - 2005
- [j8]Serena Donnini, Alan E. Mark, André H. Juffer
, Alessandra Villa:
Incorporating the effect of ionic strength in free energy calculations using explicit ions. J. Comput. Chem. 26(2): 115-122 (2005) - [j7]David van der Spoel
, Erik Lindahl
, Berk Hess
, Gerrit Groenhof
, Alan E. Mark
, Herman J. C. Berendsen:
GROMACS: Fast, flexible, and free. J. Comput. Chem. 26(16): 1701-1718 (2005) - 2004
- [j6]Chris Oostenbrink
, Alessandra Villa
, Alan E. Mark
, Wilfred F. van Gunsteren:
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25(13): 1656-1676 (2004) - 2003
- [j5]Alessandra Villa, Ronen Zangi, Gilles Pieffet, Alan E. Mark:
Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin. J. Comput. Aided Mol. Des. 17(10): 673-686 (2003) - 2002
- [j4]Alessandra Villa
, Alan E. Mark
:
Calculation of the free energy of solvation for neutral analogs of amino acid side chains. J. Comput. Chem. 23(5): 548-553 (2002)
1990 – 1999
- 1999
- [j3]Heiko Schäfer, Wilfred F. van Gunsteren, Alan E. Mark:
Estimating relative free energies from a single ensemble: Hydration free energies. J. Comput. Chem. 20(15): 1604-1617 (1999) - [p1]Alan E. Mark, Heiko Schäfer, Haiyan Liu
, Wilfred F. van Gunsteren:
Estimating Relative Free Energies from a Single Simulation of the Initial State. Computational Molecular Dynamics 1999: 149-162 - [e1]Peter Deuflhard, Jan Hermans, Benedict J. Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel:
Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering 4, Springer 1999, ISBN 978-3-540-63242-9 - 1998
- [j2]Xavier Daura, Alan E. Mark, Wilfred F. van Gunsteren:
Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J. Comput. Chem. 19(5): 535-547 (1998) - 1993
- [j1]Paul R. Gerber, Alan E. Mark, Wilfred F. van Gunsteren:
An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes. J. Comput. Aided Mol. Des. 7(3): 305-323 (1993)
Coauthor Index
![](https://dblp.uni-trier.de/img/cog.dark.24x24.png)
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
Unpaywalled article links
Add open access links from to the list of external document links (if available).
Privacy notice: By enabling the option above, your browser will contact the API of unpaywall.org to load hyperlinks to open access articles. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Unpaywall privacy policy.
Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the of the Internet Archive (if available).
Privacy notice: By enabling the option above, your browser will contact the API of archive.org to check for archived content of web pages that are no longer available. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Internet Archive privacy policy.
Reference lists
Add a list of references from ,
, and
to record detail pages.
load references from crossref.org and opencitations.net
Privacy notice: By enabling the option above, your browser will contact the APIs of crossref.org, opencitations.net, and semanticscholar.org to load article reference information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Crossref privacy policy and the OpenCitations privacy policy, as well as the AI2 Privacy Policy covering Semantic Scholar.
Citation data
Add a list of citing articles from and
to record detail pages.
load citations from opencitations.net
Privacy notice: By enabling the option above, your browser will contact the API of opencitations.net and semanticscholar.org to load citation information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the OpenCitations privacy policy as well as the AI2 Privacy Policy covering Semantic Scholar.
OpenAlex data
Load additional information about publications from .
Privacy notice: By enabling the option above, your browser will contact the API of openalex.org to load additional information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the information given by OpenAlex.
last updated on 2024-05-08 21:51 CEST by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint