Martins work with Corwin Hansch led to her ongoing work in QSAR, using computers to develop both 2D and 3D models capturing the chemical and biological properties of molecules.  As an early proponent of computational chemistry and its use in drug design, she developed combinatorial chemistry and molecular graphics techniques and was involved in the development of software packages for pharmacophore analysis such as DISCO and ALADDIN. Her work has directly affected modern day drug discovery and supported the computer design of novel compounds.  Martin has particularly focused on identifying properties of molecules relevant to biological activity, including their potency, binding affinity, and ADME properties.  Her methods have been applied to the study of diseases including hypertension, Parkinsons disease, ulcers, bacterial infections, arthritis, and angina.
She has also significantly contributed to the development of compound collections and combinatorial libraries which investigators can use to develop and compare measures of molecular similarity and diversity. Her collection of MAO (monoamine oxidase) inhibitors has been widely used by researchers.