Computational Discovery Desktop (CDD) is an applicationindependent middleware that aids researchers in the daily interaction with distributed HPC resources. It provides computational project management at personal, research group, and inter-institutional collaboration levels. The CDD framework seamlessly integrates typical operations, including multi-user access to the project data, application deployment, input preparation, job scheduling, state gathering, data archival, etc. into the daily work of the researcher by offering a common interface to the frequently performed tasks. The implemented scheduling options support an extensive logic for job dependencies and submitting and cancelling a job at specific time and condition. The job state monitor ascertains the job progress and includes the ability to terminate the job if a predefined condition is met, e.g. the job is too slow due to system issues. The interface can easily be expanded to include additional operations. The users are free to choose the desired level of integration of their dayto- day operations into the CDD framework based on their individual habits and experience of interaction with HPC resources. CDD relies on a relational MySQL database backend. It uses cron utility to perform the scheduled offline tasks and to create periodic reports about job and project states. CDD uses XML format to manage the input files and to store the post-processed metadata. It comes with an extensive set of command-line tools for interaction with the user, which are written in Perl to simplify modification and to avoid compilation. CDD employs Globus Toolkit to conduct the certificate-based authentication and data transfer. Currently configured applications include NAMD, Amber, GROMACS, LAMMPS, and NWChem. The applications were tested on NCSA Blue Waters and TACC Stampede.