AlaScan: A graphical user interface for alanine scanning free-energy calculations. Computation of the free-energy changes that underlie molecular recognition and association has gained significant importance due to its considerable potential in drug discovery. The massive increase of computational power in recent years substantiates the application of more accurate theoretical methods for the calculation of binding free energies. The impact of such advances is the application of parent approaches, like computational alanine scanning, to investigate in silico the effect of aminoacid replacement in protein−ligand and protein−protein complexes, or probe the thermostability of individual proteins. Because human effort represents a significant cost that precludes the routine use of this form of free-energy calculations, minimizing manual intervention constitutes a stringent prerequisite for any such systematic computation. With this objective in mind, we propose a new plug-in, referred to as AlaScan, developed within the popular visualization program VMD to automate the major steps in alanine-scanning calculations, employing free-energy perturbation as implemented in the widely used molecular dynamics code NAMD. The AlaScan plug-in can be utilized upstream, to prepare input files for selected alanine mutations. It can also be utilized downstream to perform the analysis of different alanine-scanning calculations and to report the free-energy estimates in a user-friendly graphical user interface, allowing favorable mutations to be identified at a glance. The plug-in also assists the end-user in assessing the reliability of the calculation through rapid visual inspection. Journal of Chemical Information and Theory, 2016.

Recent publications

The lubricating role of water in the shuttling of rotaxanes
Haohao Fu; Xueguang Shao; Christophe Chipot; Wensheng Cai;
Chem. Sci. (2017) 139 (7): 293-5094

The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations
Tanfeng Zhao; Haohao Fu; Tony Lelievre; Xueguang Shao; Christophe Chipot; Wensheng Cai;
Journal of Chemical Theory and Computation (2017) 13 (4): 1566-1576

Tribute to Klaus Schulten
Emad Tajkhorshid; Christophe Chipot;
The Journal of Physical Chemistry B (2017) 121 (15): 3203-3205


- Renewal of the Laboratoire International Associé CNRS-University of Illinois at Urbana-Champaign on November 2016
- An update of ParseFEP is available in the latest version of VMD.
- 新的分子动力学讲义 (Dissemination).


Laboratoire International Associé
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