Rejected from International Journal of Molecular Sciences? The 6 Best Journals to Submit Next

The most common rejection reason at IJMS is weak methodology. Insufficient sample sizes, missing controls, inappropriate statistical tests, and unreproducible protocols are flagged frequently. Because IJMS receives papers from a wide range of research environments globally, the editorial team has developed efficient screening for these issues. If the reviewers cited methodological concerns, those concerns are almost certainly valid and need to be addressed.

IJMS has a diverse international author base, and language quality is a genuine barrier to publication. Papers with frequent grammatical errors, unclear sentence structure, or ambiguous scientific descriptions are rejected or returned for language editing. Unlike some journals that accept papers contingent on language revision, IJMS sometimes rejects outright if the language issues are severe enough that reviewers can't evaluate the science.

Despite its broad title, IJMS focuses on molecular-level science. Papers that are purely clinical, purely computational without molecular validation, or purely engineering without molecular insight may fall outside the scope. The "molecular sciences" in the title means the journal wants molecular mechanisms, molecular interactions, or molecular characterization as the core of the paper.

IJMS publishes many special issues with guest editors. If you submitted to a special issue, the guest editors have specific expectations for the collection they're building. Rejection from a special issue doesn't mean the paper is weak overall. It may mean it didn't fit the guest editor's vision for that particular issue.

Before choosing your next journal, a International Journal of Molecular Sciences manuscript fit check can tell you whether the issue was scope or something more fundamental to address first.

1. PLOS ONE

PLOS ONE is the most broadly accessible alternative for any molecular sciences paper. The journal evaluates scientific validity and methodological soundness rather than novelty or perceived impact, which means a well-designed study that IJMS rejected for "insufficient novelty" can find a home here. PLOS ONE's acceptance rate (~50%) is comparable to IJMS's, but the review criteria are different. The APC ($2,477) is lower than most alternatives, and the journal's open-access model ensures broad visibility.

Best for: Methodologically sound papers with incremental results, confirmatory studies, any molecular science discipline.

2. Molecules

Molecules is another MDPI journal, focused on chemistry and chemical biology, including natural products, synthetic chemistry, and molecular interactions. If your IJMS paper had a chemistry angle, Molecules may be a more targeted scope match. The editorial process is similar to IJMS (same publisher, similar timeline), and the impact factor (~4) is comparable. If IJMS rejected your paper for scope reasons, Molecules may be the right MDPI journal for your specific topic.

Best for: Natural product chemistry, drug design, chemical biology, molecular interactions and recognition.

3. International Journal of Biological Macromolecules

IJBM publishes research on biological macromolecules: proteins, nucleic acids, polysaccharides, and lipids. The impact factor (~7) is higher than IJMS, so this is a step up if your paper is strong enough. The journal is published by Elsevier and has a well-established reputation in biochemistry and biopolymer science. If your IJMS paper focused on protein characterization, enzyme kinetics, or polysaccharide properties, IJBM's specialized scope gives you access to reviewers who understand the work deeply.

Best for: Protein biochemistry, polysaccharide characterization, enzyme studies, biopolymer applications.

4. Cells

Cells (MDPI) focuses on cell biology at the molecular level, covering cell signaling, cell death, organelle biology, and cellular disease mechanisms. If your IJMS paper was cell biology research with molecular characterization, Cells may be a better scope fit. The impact factor (~5) is comparable, and the editorial process is familiar if you've already submitted to IJMS. Cells is growing quickly and has established a solid reputation in the cell biology community.

Best for: Cell signaling, apoptosis and autophagy, organelle function, cellular disease mechanisms.

5. Biomolecules

Biomolecules (MDPI) covers the structure, function, and interactions of biological molecules, with emphasis on proteins, enzymes, and nucleic acids. The scope is narrower than IJMS, which can be an advantage. Your paper competes against a smaller pool of submissions, and the reviewers are specifically interested in biomolecular science. For structural biology, enzymology, and protein-protein interaction studies that IJMS rejected, Biomolecules is a natural alternative.

Best for: Protein structure and function, enzyme mechanisms, nucleic acid biochemistry, molecular interactions.

6. Frontiers in Molecular Biosciences

Frontiers in Molecular Biosciences covers molecular biology, structural biology, and bioinformatics. The Frontiers editorial model uses a collaborative review process where authors and reviewers interact directly, which can be more constructive than traditional peer review. If IJMS reviewers gave you feedback that seemed misaligned with your paper's goals, Frontiers' interactive process may lead to a more productive review. The impact factor (~4) is comparable.

Best for: Molecular biology, structural biology, bioinformatics, molecular mechanisms of disease.

Rejected for methodology? Fix every methodological issue before submitting anywhere. Add the missing controls, increase sample sizes if possible, and get a statistician to review your analysis. Methodological problems don't disappear at a new journal.

Rejected for language quality? Invest in professional English editing. This isn't optional. If IJMS flagged language issues, every other journal will see the same problems. Professional editing services typically cost $200-500 and save months of rejection-revision cycles.

Rejected from a special issue? Submit as a regular article to IJMS (if the rejection letter allows it), or send it to one of the alternative journals listed above. Special issue rejections often reflect the guest editor's preferences rather than the paper's quality.

Rejected for "insufficient novelty"? PLOS ONE evaluates validity rather than novelty. Alternatively, consider whether the paper's contribution is actually more specialized than IJMS's broad scope. A focused journal like Biomolecules or Cells may see more novelty in work that IJMS considered routine.

Paper is stronger than you initially thought? If IJMS rejected for scope rather than quality, and you now realize the work is more significant than an IJMS-level paper, consider submitting to International Journal of Biological Macromolecules (IF ~7) or even a higher-tier journal in your specific field.

Get your methods section right. Describe every protocol in enough detail that another lab could reproduce your work. Include catalog numbers for reagents, specific instrument models, and exact software versions for analysis. IJMS and its alternatives are all tightening their standards for reproducibility.

Invest in language editing. Professional editing is the single highest-return investment for papers rejected on language grounds. Don't rely on co-authors who are also non-native English speakers to catch language issues. An external editor brings fresh eyes and native fluency.

Check your figures. Are they clear at the size they'll appear in the published article? Are the labels readable? Are the error bars defined? Figure quality is the first thing editors notice when scanning a submission, and poor figures create a negative first impression that's hard to overcome.

Verify your statistical analysis. If you're using t-tests, make sure the data meets the assumptions. If you're doing multiple comparisons, apply the appropriate correction. If your sample size is small, acknowledge the limitation and consider non-parametric alternatives. Statistical errors are the most common preventable rejection reason across all molecular science journals.

Every rejection is an opportunity to make the paper stronger, but only if you actually use the feedback. Before submitting to the next journal, run your manuscript through a manuscript scope and readiness check to identify remaining formatting, methodology, and scope alignment issues. Catching problems before reviewers do is always faster than going through another review cycle.

Resubmit to the same tier if:

• Reviewers praised the science but identified fixable issues
• The rejection letter mentioned "consider resubmission after revision"
• You can address every concern within 2-3 months
• No competing paper has appeared since your submission

Move to a different journal if:

• The rejection cited scope mismatch, not quality
• Multiple reviewers questioned novelty or significance
• Your timeline needs a decision within 2-3 months
• A specialist journal's readership would value the work more

Reframe before resubmitting anywhere if:

• Reviewers found fundamental methodology concerns
• The narrative needs restructuring, not just editing
• New experiments or analyses are needed
• The rejection exposed a gap between claims and evidence

In our pre-submission review work with manuscripts targeting International Journal of Molecular Sciences, four patterns generate the most consistent desk rejections worth knowing before resubmission.

Scope outside molecular sciences: studies without molecular-level investigation. IJMS publishes work with explicit molecular characterization of biological phenomena. We see this failure as the most common pattern in IJMS desk rejections we review: papers reporting clinical outcomes, epidemiological associations, or physiological measurements without any molecular-level analysis of the underlying mechanism. In our review of IJMS submissions, we find that editors consistently require that the molecular dimension be the primary contribution of the study, not a secondary add-on.

Methodological reporting gaps that prevent reproducibility assessment. IJMS requires detailed methods sections that allow independent replication. We see this pattern in IJMS submissions we review with missing cell line authentication documentation, absent antibody catalog numbers or validation data, or PCR primer sequences not provided. These reporting gaps generate desk returns before peer review can assess the scientific conclusions.

Absence of appropriate controls that would validate the molecular assay results. IJMS reviewers screen carefully for experimental controls in molecular biology studies. We see this pattern in IJMS submissions we review: western blot studies without loading controls, gene expression studies without reference gene validation, or protein interaction studies without IgG isotype controls. Papers with missing controls face consistent editorial concerns about the validity of the molecular data.

Conclusions overstated relative to the experimental model used. IJMS editors require that the conclusions drawn from in vitro molecular studies be appropriately qualified relative to in vivo biology. We see this failure regularly in manuscripts we review: papers using one or two cell lines to draw conclusions about disease mechanisms in vivo, or identifying a molecular target in a model system and concluding therapeutic relevance without any validation in a more physiologically relevant context.

SciRev community data for International Journal of Molecular Sciences confirms desk rejections typically arrive within days, with post-review first decisions within 4-8 weeks, consistent with the MDPI editorial cadence for this multidisciplinary molecular sciences journal.