diff --git a/build.gradle b/build.gradle
index 7eda28a6..9f94b083 100644
--- a/build.gradle
+++ b/build.gradle
@@ -33,6 +33,9 @@ repositories {
     mavenCentral()
     mavenLocal()
     maven {url "https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/" }
+    maven {
+        url = file('lib/local-mvn-repo')
+    }
     flatDir(dirs: 'lib')
 }
 
diff --git a/lib/biojava-structure-6.1.0-rdk1.jar b/lib/local-mvn-repo/org/biojava/biojava-structure/6.1.0-rdk1/biojava-structure-6.1.0-rdk1.jar
similarity index 100%
rename from lib/biojava-structure-6.1.0-rdk1.jar
rename to lib/local-mvn-repo/org/biojava/biojava-structure/6.1.0-rdk1/biojava-structure-6.1.0-rdk1.jar
diff --git a/lib/local-mvn-repo/org/biojava/biojava-structure/6.1.0-rdk1/biojava-structure-6.1.0-rdk1.pom b/lib/local-mvn-repo/org/biojava/biojava-structure/6.1.0-rdk1/biojava-structure-6.1.0-rdk1.pom
new file mode 100644
index 00000000..7b6c0828
--- /dev/null
+++ b/lib/local-mvn-repo/org/biojava/biojava-structure/6.1.0-rdk1/biojava-structure-6.1.0-rdk1.pom
@@ -0,0 +1,184 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<artifactId>biojava</artifactId>
+		<groupId>org.biojava</groupId>
+		<version>6.1.0</version>
+	</parent>
+	<artifactId>biojava-structure</artifactId>
+	<name>biojava-structure</name>
+	<version>6.1.0-rdk1</version>
+	<description>The protein structure modules of BioJava.</description>
+	<licenses>
+		<license>
+			<name>GNU LGPL v2</name>
+			<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
+			<distribution>repo</distribution>
+		</license>
+	</licenses>
+
+	<dependencies>
+		<dependency>
+			<groupId>org.rcsb</groupId>
+			<artifactId>${ciftools.artifact}</artifactId>
+			<version>${ciftools.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.rcsb</groupId>
+			<artifactId>mmtf-api</artifactId>
+			<version>${mmtf.version}</version>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.rcsb</groupId>
+			<artifactId>mmtf-serialization</artifactId>
+			<version>${mmtf.version}</version>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.rcsb</groupId>
+			<artifactId>mmtf-codec</artifactId>
+			<version>${mmtf.version}</version>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.biojava</groupId>
+			<artifactId>biojava-alignment</artifactId>
+			<version>6.1.0</version>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.biojava</groupId>
+			<artifactId>biojava-core</artifactId>
+			<version>6.1.0</version>
+			<scope>compile</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>java3d</groupId>
+			<artifactId>vecmath</artifactId>
+			<version>1.3.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.jgrapht</groupId>
+			<artifactId>jgrapht-core</artifactId>
+			<!-- Pin! Java 8 requires 1.4.0 -->
+			<version>1.4.0</version>
+		</dependency>
+
+		<!-- JAXb explicit dependency is needed since Java 9. See https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j
+		  Note versions are set in parent pom in dependency management section -->
+		<dependency>
+			<groupId>javax.xml.bind</groupId>
+			<artifactId>jaxb-api</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.glassfish.jaxb</groupId>
+			<artifactId>jaxb-runtime</artifactId>
+		</dependency>
+
+		<!-- Used for json deserialization in PDBStatus -->
+		<dependency>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
+			<version>2.13.4.2</version>
+		</dependency>
+		<!-- logging dependencies (managed by parent pom, don't set versions or
+			scopes here) -->
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>slf4j-api</artifactId>
+		</dependency>
+		<!-- binding for log4j2, scope=runTime set in parent pom -->
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-slf4j-impl</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-api</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-core</artifactId>
+		</dependency>
+		<!--  Testing related dependencies -->
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>xmlunit</groupId>
+			<artifactId>xmlunit</artifactId>
+			<version>1.6</version>
+			<scope>test</scope>
+		</dependency>
+		<!-- Junit5 dependencies, defined in parent pom. -->
+		<dependency>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-engine</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-params</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.junit.vintage</groupId>
+			<artifactId>junit-vintage-engine</artifactId>
+		</dependency>
+
+	</dependencies>
+
+	<properties>
+		<maven.build.timestamp.format>yyyyMMdd-HHmm</maven.build.timestamp.format>
+		<timestamp>${maven.build.timestamp}</timestamp>
+	</properties>
+	<build>
+
+		<plugins>
+
+			<!-- Excluding demo package is required for avoiding namespace clashes
+				(demo package is in all modules) for signing the jar. See issue #387 -->
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-jar-plugin</artifactId>
+				<configuration>
+					<excludes>
+						<exclude>demo/**</exclude>
+					</excludes>
+				</configuration>
+			</plugin>
+
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-resources-plugin</artifactId>
+			</plugin>
+
+		</plugins>
+		<resources>
+			<resource>
+				<directory>src/main/resources</directory>
+				<filtering>true</filtering>
+				<includes>
+					<include>**/*.properties</include>
+				</includes>
+			</resource>
+			<resource>
+				<directory>src/main/resources</directory>
+				<filtering>false</filtering>
+				<includes>
+					<include>**/*.cif.gz</include>
+					<include>**/*.pdb.gz</include>
+					<include>**/*.mat</include>
+					<include>**/*.xml</include>
+				</includes>
+			</resource>
+		</resources>
+
+	</build>
+
+
+</project>
\ No newline at end of file
diff --git a/lib/readme.txt b/lib/readme.txt
index facf3750..f6da4796 100644
--- a/lib/readme.txt
+++ b/lib/readme.txt
@@ -9,4 +9,5 @@ https://code.google.com/archive/p/fast-random-forest/
 https://github.com/rdk/FasterForest
 
 
+local-mvn-repo is here to temporary hold jars and poms of modified libraries.