diff --git a/packages/core/src/molecule/addMoleculeValidation.test.ts b/packages/core/src/molecule/addMoleculeValidation.test.ts
index 10ef3ba5..46632b29 100644
--- a/packages/core/src/molecule/addMoleculeValidation.test.ts
+++ b/packages/core/src/molecule/addMoleculeValidation.test.ts
@@ -68,6 +68,75 @@ describe('parseMolecules()', () => {
       }
     )
   })
+
+  it('should not error on null values in molecules array', () => {
+    // when null value passed in array
+    const mockGlobalParameters = {
+      molecules: [null] as any
+    }
+    const mockGlobalSchema: JSONSchema7 = {
+      type: 'object',
+      properties: {
+        molecules: {
+          title: 'Input Molecules',
+          description: 'The input molecules that will be used for docking.',
+          $comment: 'Molecules must be provided in PDB format. These PDB files can be single molecules or ensembles using the MODEL/ENDMDL statements.',
+          type: 'array',
+          minItems: 1,
+          maxItems: 20,
+          items: {
+            type: 'string',
+            format: 'uri-reference'
+          },
+          format: 'moleculefilepaths'
+        }
+      },
+      additionalProperties: false
+    }
+    const mockFiles = {}
+
+    // return empty array
+    const actual1 = parseMolecules(
+      mockGlobalParameters,
+      mockGlobalSchema,
+      mockFiles
+    )
+    expect(actual1).toEqual([[], 'molecules'])
+  })
+  it('should not error on undefined values in molecules array', () => {
+    // when undefined value passed in array
+    const mockGlobalParameters = {
+      molecules: [undefined] as any
+    }
+    const mockGlobalSchema: JSONSchema7 = {
+      type: 'object',
+      properties: {
+        molecules: {
+          title: 'Input Molecules',
+          description: 'The input molecules that will be used for docking.',
+          $comment: 'Molecules must be provided in PDB format. These PDB files can be single molecules or ensembles using the MODEL/ENDMDL statements.',
+          type: 'array',
+          minItems: 1,
+          maxItems: 20,
+          items: {
+            type: 'string',
+            format: 'uri-reference'
+          },
+          format: 'moleculefilepaths'
+        }
+      },
+      additionalProperties: false
+    }
+    const mockFiles = {}
+
+    // return empty array
+    const actual1 = parseMolecules(
+      mockGlobalParameters,
+      mockGlobalSchema,
+      mockFiles
+    )
+    expect(actual1).toEqual([[], 'molecules'])
+  })
 })
 
 describe('addMoleculeValidation()', () => {
diff --git a/packages/core/src/molecule/addMoleculeValidation.ts b/packages/core/src/molecule/addMoleculeValidation.ts
index 78b107fd..446e92a2 100644
--- a/packages/core/src/molecule/addMoleculeValidation.ts
+++ b/packages/core/src/molecule/addMoleculeValidation.ts
@@ -20,6 +20,7 @@ export function parseMolecules (
   if (globalSchema.properties === undefined) {
     return [[], undefined]
   }
+
   // find prop which has format:moleculefilepaths
   const moleculesPropNameAndSchema = Object.entries(
     globalSchema.properties
@@ -42,8 +43,13 @@ export function parseMolecules (
   // find file of molecule path
   // TODO check whether files are actually PDB files using uiSchema.molecules..items.ui:options.accept: .pdb
   const moleculeFiles = moleculeFilePaths
-    // ignore undefined entries (invalid entries)
-    .filter(file => file !== undefined)
+    // ignore undefined/null entries (invalid entries)
+    .filter(file => {
+      // check on undefined value in array incl. string value
+      if (typeof file === 'undefined') return false
+      // check for null value
+      return file !== null
+    })
     .map((p) => files[p])
 
   // parse file