Journals to Consider

Impact FactorJournalNotes
43.113 (2015)Nature Biotechnology
38.138 (2015)Nature
37.369 (2015)Chemical Reviews
34.661 (2015)Science
30.357 (2015)Nature Medicine
28.710 (2015)Cell
25.328 (2015)Nature Methods
13.038 (2015)Journal of the American Chemical Society
11.840 (2015)Trends in Pharmacological Sciences
11.329 (2015)Nature Communications
10.162 (2016)Nucleic Acids ResearchWide variety of articles. Published NGL Viewer, web-based viewer, in 2015.
9.423 (2015)Proceedings of the National Academy of Sciences
7.870 (2015)Cell Reports
6.713 (????)Current Opinion in Structural Biology
6.302 (2017)Briefings in BioinformaticsBriefings in Bioinformatics is a review journal and does not publish original research.
5.618 (2014)Structure
5.589 (2015)Journal of Medicinal Chemistry
5.481 (2017)BioinformaticsBioPython, ProDy published here. Other python packages. Genetics papers too. Good choice for high-end bioinformatics projects. 3dmol.js published here in 2015.
5.301 (2015)Journal of Chemical Theory and ComputationSome methods development, including Python packages, but mostly geared towards MD and QM.
5.595 (????)The Faseb JournalSome MD articles.
5.259 (2015)British Journal of Pharmacology
5.246 (2016)BiomacromoleculesHas some MD simulations. Search here.
5.228 (2015)Scientific Reports
5.090 (2015)ACS Chemical Biology
4.587 (2015)PLoS Computational BiologyMethods articles and Software articles require presubmission inquiries. “Outstanding open source software of exceptional importance that has been shown to provide new biological insights.”
4.333 (2014)Journal of Molecular Biology
4.031 (????)Frontiers in Physiology
4.220 (2016)Journal of CheminformaticsLot’s of papers about databases, tools, methods, virtual-screening methods, etc. Seems right up your alley. Open Babel and Avrogado published here. Has software articles. Note that I couldn’t find many VS-results publications, but the stated scope of the journal includes “computer-aided molecular design” and “QSAR.”
4.125 (2016)Journal of Biological ChemistrySome MD and docking papers. Good for papers with solid prospective experimental validation.
3.948 (2015)PLOS Neglected Tropical Diseases
3.748 (2017)Computer Physics Communications
3.657 (2015)Journal of Chemical Information and ModelingWeb-apps, methods, virtual screening, with specific application papers too.
3.648 (2015)Journal of Computational ChemistryMDAnalysis published here. Simulations. Lots of quantum. Not too much virtual screening. Chimera published here.
3.632 (2015)Biophysical Journal
3.539 (2014)Expert Opinion on Drug DiscoveryAppears to be mostly reviews.
3.447 (2014)European Journal of Medicinal Chemistry
3.402 (2014)Current Topics in Medicinal ChemistryReviews.
3.355 (2015)ACS Medicinal Chemistry LettersSome recent VS-results papers too**.
3.556 (2016)Future Medicinal ChemistryWeb servers, virtual screening, and non computational stuff too.
3.234 (2014)Plos One
3.226 (2016)International Journal of Molecular SciencesSome MD, docking, etc.
3.199 (????)Journal of Computer-aided Molecular DesignLot’s of modeling and CADD. In silico + in vitro studies.
3.187 (2015)The Journal of Physical Chemistry B
3.123 (2016)Journal of Biomolecular Structure and DynamicsRecently published the results of a virtual screen.
3.052 (????)Current Pharmaceutical DesignReviews only?
3.028 (2014)Drug Design, Development and TherapyRecently published results of a virtual screen.
3.025 (2015)Chemical Research in ToxicologyStudies of the development and application of new methodologies for the investigation of the interaction of toxic agents with living systems.
2.980 (2015)ChemMedChemRecently published some virtual screens.
2.876 (2015)Biochemistry
2.829 (????)Molecular BioSystems
2.802 (2015)Chemical Biology & Drug DesignMixture of experimental and computation. Some mixed (virtual screening + testing). Some simulation papers.
2.570 (2015)Journal of Structural Biology
2.774 (2017)ChemBioChem
2.499 (2015)Proteins: Structure, Function, and BioinformaticsLots of simulation and structure papers.
2.495 (2014)MedChemCommLots of testing specific compounds and demonstrating activity. Synthesis heavy, with CADD contributions.
2.486 (2015)Bioorganic & Medicinal Chemistry LettersSeems like mostly a synthesis journal. But VS results recently published.
2.435 (????)BMC Bioinformatics“Computational and statistical methods for the modeling and analysis of all kinds of biological data.” Very broad. Few articles like yours, but might accept. BioBlender paper.
3.123 (2016)Journal of Biomolecular Structure and DynamicsQuite a few virtual-screening articles. Very structural.
2.42 (2014)Bioorganic Medicinal Chemistry Letters
2.402 (2016)Biophysical Chemistry
2.091 (2015)Journal of Molecular RecognitionSome docking and simualtion.
2.030 (????)BMC Pharmacology and Toxicology
1.943 (2014)Communications in Computational Physics
1.884 (2016)Journal of Chemometrics
1.758 (2015)Chemical Physics
1.674 (2015)Journal of Molecular Graphics and ModellingLots of simulation and docking.
1.225 (2015)Journal of Chemical Education
1.014 (????)Computational Biology and Chemistry

A very helpful list can be found here. Also here to a lesser extent.