<?xml version="1.0" encoding="utf-8"?>
<!--XBRL document created with Toppan Merrill Bridge  11.4.0.1 -->
<!--Based on XBRL 2.1-->
<!--Created on: 8/6/2026 8:14:16 PM-->
<!--Modified on: 8/6/2026 8:14:16 PM-->
<xsd:schema targetNamespace="http://structuretx.com/20260630" attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:dei="http://xbrl.sec.gov/dei/2026" xmlns:deprecated="http://www.xbrl.org/2009/role/deprecated" xmlns:dtr="http://www.xbrl.org/2009/dtr" xmlns:ref="http://www.xbrl.org/2006/ref" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xl="http://www.xbrl.org/2003/XLink" xmlns:us-gaap="http://fasb.org/us-gaap/2026" xmlns:utr="http://www.xbrl.org/2009/utr" xmlns:stpr="http://xbrl.sec.gov/stpr/2026" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:enum2="http://xbrl.org/2020/extensible-enumerations-2.0" xmlns:us-roles="http://fasb.org/us-roles/2026" xmlns:net="http://www.xbrl.org/2009/role/net" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:dtr-types="http://www.xbrl.org/dtr/type/2024-01-31" xmlns:xbrldi="http://xbrl.org/2006/xbrldi" xmlns:negated="http://www.xbrl.org/2009/role/negated" xmlns:srt="http://fasb.org/srt/2026" xmlns:attributeFormDefault="unqualified" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:gpcr="http://structuretx.com/20260630" xmlns:ecd="http://xbrl.sec.gov/ecd/2026" xmlns:ecd-sub="http://xbrl.sec.gov/ecd-sub/2026">
  <xsd:annotation>
    <xsd:appinfo>
      <link:roleType roleURI="http://structuretx.com/role/StatementCondensedConsolidatedBalanceSheets" id="StatementCondensedConsolidatedBalanceSheets">
        <link:definition>995200100 - Statement - CONDENSED CONSOLIDATED BALANCE SHEETS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/StatementCondensedConsolidatedStatementsOfOperationsAndComprehensiveLoss" id="StatementCondensedConsolidatedStatementsOfOperationsAndComprehensiveLoss">
        <link:definition>995200200 - Statement - CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/StatementCondensedConsolidatedStatementsOfCashFlows" id="StatementCondensedConsolidatedStatementsOfCashFlows">
        <link:definition>995200400 - Statement - CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureSummaryOfSignificantAccountingPoliciesSegmentsDetails" id="DisclosureSummaryOfSignificantAccountingPoliciesSegmentsDetails">
        <link:definition>99940201 - Disclosure - Summary of Significant Accounting Policies - Segments (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureCompositionOfCertainConsolidatedFinancialStatementLineItemsAccruedExpensesAndOtherCurrentLiabilitiesDetails" id="DisclosureCompositionOfCertainConsolidatedFinancialStatementLineItemsAccruedExpensesAndOtherCurrentLiabilitiesDetails">
        <link:definition>99940301 - Disclosure - Composition of Certain Consolidated Financial Statement Line Items - Accrued expenses and other current liabilities (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureFairValueMeasurementsFairValueToAmortizedCostDetails" id="DisclosureFairValueMeasurementsFairValueToAmortizedCostDetails">
        <link:definition>99940402 - Disclosure - Fair Value Measurements - Fair value to amortized cost (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureCommitmentsAndContingenciesMaturitiesOfOperatingLeaseLiabilitiesDetails" id="DisclosureCommitmentsAndContingenciesMaturitiesOfOperatingLeaseLiabilitiesDetails">
        <link:definition>99940501 - Disclosure - Commitments and Contingencies - Maturities of operating lease liabilities (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureCommitmentsAndContingenciesMaturitiesOfOperatingLeaseLiabilitiesDetailsCalc2" id="DisclosureCommitmentsAndContingenciesMaturitiesOfOperatingLeaseLiabilitiesDetailsCalc2">
        <link:definition>40501 - Disclosure - Commitments and Contingencies - Maturities of operating lease liabilities (Details) (Calc2)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DocumentDocumentAndEntityInformation" id="DocumentDocumentAndEntityInformation">
        <link:definition>995200090 - Document - Document and Entity Information</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/StatementCondensedConsolidatedBalanceSheetsParenthetical" id="StatementCondensedConsolidatedBalanceSheetsParenthetical">
        <link:definition>995200105 - Statement - CONDENSED CONSOLIDATED BALANCE SHEETS (Parenthetical)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/StatementCondensedConsolidatedStatementsOfShareholdersEquity" id="StatementCondensedConsolidatedStatementsOfShareholdersEquity">
        <link:definition>995200300 - Statement - CONDENSED CONSOLIDATED STATEMENTS OF SHAREHOLDERS' EQUITY</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureShareholdersEquityTables" id="DisclosureShareholdersEquityTables">
        <link:definition>99930603 - Disclosure - Shareholders' Equity (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureOrganizationAndNatureOfBusinessDetails" id="DisclosureOrganizationAndNatureOfBusinessDetails">
        <link:definition>99940101 - Disclosure - Organization and Nature of the Business (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureFairValueMeasurementsLevelOfFairValueHierarchyDetails" id="DisclosureFairValueMeasurementsLevelOfFairValueHierarchyDetails">
        <link:definition>99940401 - Disclosure - Fair Value Measurements - Level of the fair value hierarchy (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureCommitmentsAndContingenciesAdditionalInformationDetails" id="DisclosureCommitmentsAndContingenciesAdditionalInformationDetails">
        <link:definition>99940502 - Disclosure - Commitments and Contingencies - Additional information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureShareholdersEquityAdditionalInformationDetails" id="DisclosureShareholdersEquityAdditionalInformationDetails">
        <link:definition>99940601 - Disclosure - Shareholders' Equity - Additional information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureShareholdersEquityScheduleOfRecognizedShareBasedCompensationDetails" id="DisclosureShareholdersEquityScheduleOfRecognizedShareBasedCompensationDetails">
        <link:definition>99940602 - Disclosure - Shareholders' Equity - Schedule of recognized share-based compensation (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureShareholdersEquityScheduleOfRecognizedShareBasedCompensationDefaultDetails" id="DisclosureShareholdersEquityScheduleOfRecognizedShareBasedCompensationDefaultDetails">
        <link:definition>40602 - Disclosure - Shareholders' Equity - Schedule of recognized share-based compensation Default (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureLicenseAgreementDetails" id="DisclosureLicenseAgreementDetails">
        <link:definition>99940701 - Disclosure - License Agreement (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureAssetPurchaseAgreementDetails" id="DisclosureAssetPurchaseAgreementDetails">
        <link:definition>99940801 - Disclosure - Asset Purchase Agreement (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureCollaborationAgreementsDetails" id="DisclosureCollaborationAgreementsDetails">
        <link:definition>99940901 - Disclosure - Collaboration Agreements (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureNetLossPerShareOutstandingSharesOfPotentiallyDilutiveSecuritiesDetails" id="DisclosureNetLossPerShareOutstandingSharesOfPotentiallyDilutiveSecuritiesDetails">
        <link:definition>99941002 - Disclosure - Net Loss Per Share - Outstanding shares of potentially dilutive securities (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureOrganizationAndNatureOfBusiness" id="DisclosureOrganizationAndNatureOfBusiness">
        <link:definition>995210101 - Disclosure - Organization and Nature of the Business</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureSummaryOfSignificantAccountingPolicies" id="DisclosureSummaryOfSignificantAccountingPolicies">
        <link:definition>995210201 - Disclosure - Summary of Significant Accounting Policies</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureCompositionOfCertainConsolidatedFinancialStatementLineItems" id="DisclosureCompositionOfCertainConsolidatedFinancialStatementLineItems">
        <link:definition>995210301 - Disclosure - Composition of Certain Consolidated Financial Statement Line Items</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureFairValueMeasurements" id="DisclosureFairValueMeasurements">
        <link:definition>995210401 - Disclosure - Fair Value Measurements</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureCommitmentsAndContingencies" id="DisclosureCommitmentsAndContingencies">
        <link:definition>995210501 - Disclosure - Commitments and Contingencies</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureShareholdersEquity" id="DisclosureShareholdersEquity">
        <link:definition>995210601 - Disclosure - Shareholders' Equity</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureLicenseAgreement" id="DisclosureLicenseAgreement">
        <link:definition>995210701 - Disclosure - License Agreement</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureAssetPurchaseAgreement" id="DisclosureAssetPurchaseAgreement">
        <link:definition>995210801 - Disclosure - Asset Purchase Agreement</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureCollaborationAgreements" id="DisclosureCollaborationAgreements">
        <link:definition>995210901 - Disclosure - Collaboration Agreements</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureNetLossPerShare" id="DisclosureNetLossPerShare">
        <link:definition>995211001 - Disclosure - Net Loss Per Share</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureSummaryOfSignificantAccountingPoliciesPolicies" id="DisclosureSummaryOfSignificantAccountingPoliciesPolicies">
        <link:definition>99920202 - Disclosure - Summary of Significant Accounting Policies (Policies)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureSummaryOfSignificantAccountingPoliciesTables" id="DisclosureSummaryOfSignificantAccountingPoliciesTables">
        <link:definition>99930203 - Disclosure - Summary of Significant Accounting Policies (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureCompositionOfCertainConsolidatedFinancialStatementLineItemsTables" id="DisclosureCompositionOfCertainConsolidatedFinancialStatementLineItemsTables">
        <link:definition>99930303 - Disclosure - Composition of Certain Consolidated Financial Statement Line Items (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureFairValueMeasurementsTables" id="DisclosureFairValueMeasurementsTables">
        <link:definition>99930403 - Disclosure - Fair Value Measurements (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureCommitmentsAndContingenciesTables" id="DisclosureCommitmentsAndContingenciesTables">
        <link:definition>99930503 - Disclosure - Commitments and Contingencies (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureNetLossPerShareTables" id="DisclosureNetLossPerShareTables">
        <link:definition>99931003 - Disclosure - Net Loss Per Share (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureFairValueMeasurementsAdditionalInformationDetails" id="DisclosureFairValueMeasurementsAdditionalInformationDetails">
        <link:definition>99940403 - Disclosure - Fair Value Measurements - Additional information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://structuretx.com/role/DisclosureNetLossPerShareComputationOfBasicAndDilutedNetLossPerShareDetails" id="DisclosureNetLossPerShareComputationOfBasicAndDilutedNetLossPerShareDetails">
        <link:definition>99941001 - Disclosure - Net Loss Per Share - Computation of basic and diluted net loss per share (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:linkbaseRef xlink:type="simple" xlink:href="gpcr-20260630_pre.xml" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
      <link:linkbaseRef xlink:type="simple" xlink:href="gpcr-20260630_cal.xml" xlink:role="http://www.xbrl.org/2003/role/calculationLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
      <link:linkbaseRef xlink:type="simple" xlink:href="gpcr-20260630_def.xml" xlink:role="http://www.xbrl.org/2003/role/definitionLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
      <link:linkbaseRef xlink:type="simple" xlink:href="gpcr-20260630_lab.xml" xlink:role="http://www.xbrl.org/2003/role/labelLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
      <link:roleType roleURI="http://structuretx.com/role/DisclosureStandardAndCustomAxisDomainDefaults" id="DisclosureStandardAndCustomAxisDomainDefaults">
        <link:definition>99900 - Disclosure - Standard And Custom Axis Domain Defaults</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
    </xsd:appinfo>
  </xsd:annotation>
  <xsd:import namespace="https://xbrl.org/2023/calculation-1.1" schemaLocation="https://www.xbrl.org/2023/calculation-1.1.xsd" />
  <xsd:import namespace="http://xbrl.sec.gov/ecd/2026" schemaLocation="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd" />
  <xsd:import namespace="http://xbrl.sec.gov/stpr/2026" schemaLocation="https://xbrl.sec.gov/stpr/2026/stpr-2026.xsd" />
  <xsd:import namespace="http://www.xbrl.org/2009/role/negated" schemaLocation="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd" />
  <xsd:import namespace="http://www.xbrl.org/2003/instance" schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd" />
  <xsd:import namespace="http://xbrl.org/2005/xbrldt" schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd" />
  <xsd:import namespace="http://xbrl.sec.gov/dei/2026" schemaLocation="https://xbrl.sec.gov/dei/2026/dei-2026.xsd" />
  <xsd:import namespace="http://fasb.org/us-gaap/2026" schemaLocation="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd" />
  <xsd:import namespace="http://fasb.org/srt/2026" schemaLocation="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd" />
  <xsd:import namespace="http://www.xbrl.org/dtr/type/2024-01-31" schemaLocation="https://www.xbrl.org/dtr/type/2024-01-31/types.xsd" />
  <xsd:import namespace="http://fasb.org/us-roles/2026" schemaLocation="https://xbrl.fasb.org/us-gaap/2026/elts/us-roles-2026.xsd" />
  <xsd:import namespace="http://xbrl.sec.gov/ecd-sub/2026" schemaLocation="https://xbrl.sec.gov/ecd/2026/ecd-sub-2026.xsd" />
  <xsd:element name="SchrodingerInc.Member" id="gpcr_SchrodingerInc.Member" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="SoftwarePlatformUseForResearchPurposesMember" id="gpcr_SoftwarePlatformUseForResearchPurposesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="AccruedExpensesAndOtherLiabilitiesCurrent" id="gpcr_AccruedExpensesAndOtherLiabilitiesCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" xbrli:balance="credit" />
  <xsd:element name="InterestAndOtherIncomeExpenseNet" id="gpcr_InterestAndOtherIncomeExpenseNet" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="credit" />
  <xsd:element name="IncreaseDecreaseInAccruedExpensesAndOtherCurrentLiabilities" id="gpcr_IncreaseDecreaseInAccruedExpensesAndOtherCurrentLiabilities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="debit" />
  <xsd:element name="NonCashLeaseExpense" id="gpcr_NonCashLeaseExpense" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="debit" />
  <xsd:element name="RiskAndUncertaintiesPolicyPolicyTextBlock" id="gpcr_RiskAndUncertaintiesPolicyPolicyTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="ScheduleOfAccruedExpensesAndOtherCurrentLiabilitiesTableTextBlock" id="gpcr_ScheduleOfAccruedExpensesAndOtherCurrentLiabilitiesTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="AccruedResearchAndDevelopmentExpensesCurrent" id="gpcr_AccruedResearchAndDevelopmentExpensesCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" xbrli:balance="credit" />
  <xsd:element name="AccruedClinicalExpensesCurrent" id="gpcr_AccruedClinicalExpensesCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" xbrli:balance="credit" />
  <xsd:element name="UnauditedInterimFinancialInformationPolicyPolicyTextBlock" id="gpcr_UnauditedInterimFinancialInformationPolicyPolicyTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="ImpairmentOfMarketableSecurities" id="gpcr_ImpairmentOfMarketableSecurities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="debit" />
  <xsd:element name="LhotseCollaborationAgreementMember" id="gpcr_LhotseCollaborationAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="CollaborationAgreementDevelopmentAndRegulatoryMilestonePaymentsPayable" id="gpcr_CollaborationAgreementDevelopmentAndRegulatoryMilestonePaymentsPayable" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" xbrli:balance="credit" />
  <xsd:element name="CollaborationAgreementRoyaltyTerm" id="gpcr_CollaborationAgreementRoyaltyTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="CollaborationAgreementRoyaltyExtensionTerm" id="gpcr_CollaborationAgreementRoyaltyExtensionTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="CollaborationAgreementMilestoneOrRoyaltyPaymentsPayable" id="gpcr_CollaborationAgreementMilestoneOrRoyaltyPaymentsPayable" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" xbrli:balance="credit" />
  <xsd:element name="SaleOfStockAggregateNumberOfSharesAgreedToSell" id="gpcr_SaleOfStockAggregateNumberOfSharesAgreedToSell" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="AconcaguaCollaborationAgreementMember" id="gpcr_AconcaguaCollaborationAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="OfferingCostsIncludedInAccountsPayableAndAccruedExpensesAndOtherCurrentLiabilities" id="gpcr_OfferingCostsIncludedInAccountsPayableAndAccruedExpensesAndOtherCurrentLiabilities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="credit" />
  <xsd:element name="OptionGrantedToPurchaseMaximumNumberOfShares" id="gpcr_OptionGrantedToPurchaseMaximumNumberOfShares" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="DebtSecuritiesAvailableForSaleMaturityAllocatedAndSingleMaturityDateRollingAfterOneThroughTwoYearsFairValue" id="gpcr_DebtSecuritiesAvailableForSaleMaturityAllocatedAndSingleMaturityDateRollingAfterOneThroughTwoYearsFairValue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" xbrli:balance="debit" />
  <xsd:element name="SingleReportableSegmentMember" id="gpcr_SingleReportableSegmentMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="DiscoveryResearchAndDevelopmentExpense" id="gpcr_DiscoveryResearchAndDevelopmentExpense" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="debit" />
  <xsd:element name="ClinicalResearchAndDevelopmentExpense" id="gpcr_ClinicalResearchAndDevelopmentExpense" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="debit" />
  <xsd:element name="ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfTranches" id="gpcr_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfTranches" type="xbrli:integerItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="PerformanceBasedRestrictedStockUnitsMember" id="gpcr_PerformanceBasedRestrictedStockUnitsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="AdjustmentsToAdditionalPaidInCapitalDepositoryIssuanceCostOffset" id="gpcr_AdjustmentsToAdditionalPaidInCapitalDepositoryIssuanceCostOffset" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="credit" />
  <xsd:element name="ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfMilestones" id="gpcr_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfMilestones" type="xbrli:integerItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfMilestonesAchievementCertified" id="gpcr_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfMilestonesAchievementCertified" type="xbrli:integerItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfMilestonesAchievementProbable" id="gpcr_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfMilestonesAchievementProbable" type="xbrli:integerItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="AssetSaleInitialPayments" id="gpcr_AssetSaleInitialPayments" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="debit" />
  <xsd:element name="AssetSaleContingentMilestonePayments" id="gpcr_AssetSaleContingentMilestonePayments" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="debit" />
  <xsd:element name="SaleOfStockAuthorizedIssuanceAmount" id="gpcr_SaleOfStockAuthorizedIssuanceAmount" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" xbrli:balance="credit" />
  <xsd:element name="AtMarketCommonStockOfferingProgramMember" id="gpcr_AtMarketCommonStockOfferingProgramMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="AssetSaleAbstract" id="gpcr_AssetSaleAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="AssetSaleTextBlock" id="gpcr_AssetSaleTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="AssetSaleTable" id="gpcr_AssetSaleTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="AssetSaleLineItem" id="gpcr_AssetSaleLineItem" type="xbrli:stringItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="GrossProceedsFromIssuanceOfCommonStock" id="gpcr_GrossProceedsFromIssuanceOfCommonStock" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="debit" />
  <xsd:element name="SaleOfStockRemainingAvailableForSale" id="gpcr_SaleOfStockRemainingAvailableForSale" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" xbrli:balance="credit" />
  <xsd:element name="FollowOnOffering2025Member" id="gpcr_FollowOnOffering2025Member" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="LicenseRevenueMember" id="gpcr_LicenseRevenueMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="WarrantsIssuanceCostsAndUnderwritingDiscount" id="gpcr_WarrantsIssuanceCostsAndUnderwritingDiscount" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="debit" />
  <xsd:element name="NumberOfWarrantsIssued" id="gpcr_NumberOfWarrantsIssued" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="PreFundedWarrantsMember" id="gpcr_PreFundedWarrantsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="ClassOfWarrantOrRightPublicOfferingPriceOfWarrantsOrRights" id="gpcr_ClassOfWarrantOrRightPublicOfferingPriceOfWarrantsOrRights" type="dtr-types:perShareItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" />
  <xsd:element name="CollaborativeArrangementDisclosureAbstract" id="gpcr_CollaborativeArrangementDisclosureAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="GenentechIncMember" id="gpcr_GenentechIncMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="LicenseAgreementUpfrontPaymentReceived" id="gpcr_LicenseAgreementUpfrontPaymentReceived" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="credit" />
  <xsd:element name="LicenseAgreementThresholdNumberOfDaysOfPriorWrittenNoticeForTermination" id="gpcr_LicenseAgreementThresholdNumberOfDaysOfPriorWrittenNoticeForTermination" type="xbrli:integerItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="LicenseAgreementTransactionPrice" id="gpcr_LicenseAgreementTransactionPrice" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="credit" />
  <xsd:element name="GainLossOnDispositionOfNonFinancialAssets" id="gpcr_GainLossOnDispositionOfNonFinancialAssets" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="credit" />
  <xsd:element name="CollaborationAgreementNumberOfMilestonesAchieved" id="gpcr_CollaborationAgreementNumberOfMilestonesAchieved" type="xbrli:integerItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="WarrantsExercised" id="gpcr_WarrantsExercised" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" />
  <xsd:element name="LicenseAgreementDisclosureTextBlock" id="gpcr_LicenseAgreementDisclosureTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" />
  <xsd:element name="LicenseAgreementDisclosureAbstract" id="gpcr_LicenseAgreementDisclosureAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="AshleyHallMember" id="gpcr_AshleyHallMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="BlaiCollMember" id="gpcr_BlaiCollMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="XichenLinMember" id="gpcr_XichenLinMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="ManufacturingExpense" id="gpcr_ManufacturingExpense" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="false" xbrli:balance="debit" />
  <xsd:element name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOtherThanOptionsAggregateFairValue" id="gpcr_ShareBasedCompensationArrangementByShareBasedPaymentAwardOtherThanOptionsAggregateFairValue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" xbrli:balance="credit" />
  <xsd:element name="PerformanceShareUnits2026Member" id="gpcr_PerformanceShareUnits2026Member" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" abstract="true" />
  <xsd:element name="IncreasedSharesAvailableToBeSold" id="gpcr_IncreasedSharesAvailableToBeSold" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" abstract="false" xbrli:balance="debit" />
</xsd:schema>
