diff --git a/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild
deleted file mode 100644
index 1b0157ac30..0000000000
--- a/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild
+++ /dev/null
@@ -1,118 +0,0 @@
-# Copyright 2021-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_12 )
-BOINC_APP_OPTIONAL=1
-inherit boinc-app flag-o-matic meson optfeature python-any-r1
-
-DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
-HOMEPAGE="https://gitlab.com/Jukic/cmdock"
-SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.bz2"
-S="${WORKDIR}/${PN}-v${PV}"
-
-LICENSE="LGPL-3 ZLIB"
-SLOT="0/${PV}"
-KEYWORDS="~amd64"
-IUSE="apidoc cpu_flags_x86_sse2 doc test"
-
-# Flaky tests
-RESTRICT="test"
-
-DEPEND="
-	dev-cpp/eigen:3
-	>=dev-cpp/indicators-2.3-r1
-	>=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
-	>=dev-libs/cxxopts-3
-"
-BDEPEND="
-	apidoc? (
-		app-text/doxygen
-		dev-texlive/texlive-fontutils
-	)
-	doc? (
-		$(python_gen_any_dep '
-			dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]
-			dev-python/sphinx[${PYTHON_USEDEP}]
-		')
-	)
-	test? ( ${PYTHON_DEPS} )
-"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-include.patch
-	"${FILESDIR}"/${P}-cxxopts.patch
-)
-
-DOCS=( README.md changelog.md )
-
-BOINC_MASTER_URL="https://www.sidock.si/sidock/"
-BOINC_INVITATION_CODE="Crunch_4Science"
-BOINC_APP_HELPTEXT=\
-"The easiest way to do something useful with this application
-is to attach it to SiDock@home BOINC project."
-
-INSTALL_PREFIX="${EPREFIX}/opt/${P}"
-
-boinc-app_add_deps
-
-python_check_deps() {
-	use doc || return 0
-
-	python_has_version "dev-python/sphinx[${PYTHON_USEDEP}]" &&
-	python_has_version "dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]"
-}
-
-foreach_wrapper_job() {
-	sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
-}
-
-src_prepare() {
-	default
-	python_fix_shebang "${S}"/bin
-}
-
-src_configure() {
-	# very weird directory layout
-	local emesonargs=(
-		--prefix="${INSTALL_PREFIX:?}"
-		$(meson_use apidoc)
-		$(meson_use doc)
-		$(meson_use test tests)
-		-Ddocdir="${EPREFIX}"/usr/share/doc/${PF}
-	)
-	meson_src_configure
-
-	use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE"
-}
-
-src_install() {
-	meson_src_install
-	python_optimize "${D}${INSTALL_PREFIX:?}"/bin
-
-	if use boinc; then
-		boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r1.xml
-		boinc_install_wrapper cmdock-l_wrapper \
-			"${FILESDIR}"/cmdock-l_job_0.2.0-r1.xml cmdock-l_job.xml
-
-		# install cmdock executable
-		exeinto "$(get_project_root)"
-		exeopts --owner root --group boinc
-		doexe "${D}${INSTALL_PREFIX:?}"/bin/cmdock
-
-		# install a blank file
-		insinto "$(get_project_root)"
-		insopts -m 0644 --owner root --group boinc
-		newins - docking_out
-	fi
-}
-
-pkg_postinst() {
-	optfeature "sdtether.py and sdrmsd.py scripts" "dev-python/numpy sci-chemistry/openbabel[python]"
-	use boinc && boinc-app_pkg_postinst
-}
-
-pkg_postrm() {
-	use boinc && boinc-app_pkg_postrm
-}
diff --git a/sci-biology/cmdock/cmdock-0.2.0-r3.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r4.ebuild
similarity index 76%
rename from sci-biology/cmdock/cmdock-0.2.0-r3.ebuild
rename to sci-biology/cmdock/cmdock-0.2.0-r4.ebuild
index 394b454452..7df9beea5e 100644
--- a/sci-biology/cmdock/cmdock-0.2.0-r3.ebuild
+++ b/sci-biology/cmdock/cmdock-0.2.0-r4.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{12..13} )
+PYTHON_COMPAT=( python3_{12..14} )
 BOINC_APP_OPTIONAL=1
 inherit boinc-app flag-o-matic meson optfeature python-any-r1
 
@@ -13,18 +13,20 @@ SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.bz2"
 S="${WORKDIR}/${PN}-v${PV}"
 
 LICENSE="LGPL-3 ZLIB"
-SLOT="0/${PV}"
+SLOT="0"
 KEYWORDS="~amd64"
 IUSE="apidoc cpu_flags_x86_sse2 doc test"
 
 # Flaky tests
 RESTRICT="test"
 
+RDEPEND="dev-libs/icu:="
 DEPEND="
+	${RDEPEND}
 	dev-cpp/eigen:3
 	>=dev-cpp/indicators-2.3-r1
 	>=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
-	>=dev-libs/cxxopts-3
+	>=dev-libs/cxxopts-3.1[icu]
 "
 BDEPEND="
 	apidoc? (
@@ -48,7 +50,6 @@ PATCHES=(
 DOCS=( README.md changelog.md )
 
 BOINC_MASTER_URL="https://www.sidock.si/sidock/"
-BOINC_INVITATION_CODE="Crunch_4Science"
 BOINC_APP_HELPTEXT=\
 "The easiest way to do something useful with this application
 is to attach it to SiDock@home BOINC project."
@@ -74,13 +75,28 @@ src_prepare() {
 }
 
 src_configure() {
-	# very weird directory layout
+	mkdir "${T}/pkg-config" || die
+	export PKG_CONFIG_PATH="${T}/pkg-config${PKG_CONFIG_PATH+:${PKG_CONFIG_PATH}}"
+	cat >> "${T}/pkg-config/pcg-cpp.pc" <<-EOF || die
+		Name: pcg-cpp
+		Version: 9999
+		Description:
+	EOF
+	cat >> "${T}/pkg-config/icu-cu.pc" <<-EOF || die
+		Name: icu-cu
+		Version: 9999
+		Description:
+		Requires: icu-uc
+	EOF
+
+	# extremely weird directory layout
 	local emesonargs=(
 		--prefix="${INSTALL_PREFIX:?}"
 		$(meson_use apidoc)
 		$(meson_use doc)
 		$(meson_use test tests)
 		-Ddocdir="${EPREFIX}"/usr/share/doc/${PF}
+		-Dcpp_std=c++17
 	)
 	meson_src_configure
 
@@ -92,16 +108,16 @@ src_install() {
 	python_optimize "${D}${INSTALL_PREFIX:?}"/bin
 
 	if use boinc; then
-		boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r1.xml
-		boinc_install_wrapper cmdock-l_wrapper \
-			"${FILESDIR}"/cmdock-l_job_0.2.0-r1.xml cmdock-l_job.xml
+		boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r2.xml
+		boinc_install_wrapper cmdock_wrapper \
+			"${FILESDIR}"/sidock_job_0.2.0.xml sidock_job.xml
 
-		# install cmdock executable
+		# install the main executable
 		exeinto "$(get_project_root)"
 		exeopts --owner root --group boinc
 		doexe "${D}${INSTALL_PREFIX:?}"/bin/cmdock
 
-		# install a blank file
+		# install an empty file
 		insinto "$(get_project_root)"
 		insopts -m 0644 --owner root --group boinc
 		newins - docking_out
diff --git a/sci-biology/cmdock/files/app_info_0.2.0-r1.xml b/sci-biology/cmdock/files/app_info_0.2.0-r2.xml
similarity index 67%
rename from sci-biology/cmdock/files/app_info_0.2.0-r1.xml
rename to sci-biology/cmdock/files/app_info_0.2.0-r2.xml
index b9eb040fbd..fed302a07a 100644
--- a/sci-biology/cmdock/files/app_info_0.2.0-r1.xml
+++ b/sci-biology/cmdock/files/app_info_0.2.0-r2.xml
@@ -1,11 +1,11 @@
 <app_info>
 <app>
-	<name>cmdock-l</name>
-	<user_friendly_name>CurieMarieDock @PV@ long tasks</user_friendly_name>
+	<name>sidock</name>
+	<user_friendly_name>SiDock@home CurieMarieDock</user_friendly_name>
 </app>
 
 <file_info>
-	<name>cmdock-l_wrapper</name>
+	<name>cmdock_wrapper</name>
 	<sticky/>
 	<executable/>
 </file_info>
@@ -16,7 +16,7 @@
 </file_info>
 
 <file_info>
-	<name>cmdock-l_job.xml</name>
+	<name>sidock_job.xml</name>
 	<sticky/>
 </file_info>
 <file_info>
@@ -25,19 +25,19 @@
 </file_info>
 
 <app_version>
-	<app_name>cmdock-l</app_name>
+	<app_name>sidock</app_name>
 	<version_num>100</version_num>
 	<file_ref>
-		<file_name>cmdock-l_wrapper</file_name>
+		<file_name>cmdock_wrapper</file_name>
 		<main_program/>
 	</file_ref>
 	<file_ref>
 		<file_name>cmdock</file_name>
-		<open_name>cmdock</open_name>
+		<open_name>sidock</open_name>
 		<copy_file/>
 	</file_ref>
 	<file_ref>
-		<file_name>cmdock-l_job.xml</file_name>
+		<file_name>sidock_job.xml</file_name>
 		<open_name>job.xml</open_name>
 		<copy_file/>
 	</file_ref>
@@ -46,5 +46,6 @@
 		<open_name>docking_out</open_name>
 		<copy_file/>
 	</file_ref>
+	<is_wrapper/>
 </app_version>
 </app_info>
diff --git a/sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml b/sci-biology/cmdock/files/sidock_job_0.2.0.xml
similarity index 94%
rename from sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml
rename to sci-biology/cmdock/files/sidock_job_0.2.0.xml
index 6d626fb826..99d3627add 100644
--- a/sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml
+++ b/sci-biology/cmdock/files/sidock_job_0.2.0.xml
@@ -1,6 +1,6 @@
 <job_desc>
 	<task>
-		<application>cmdock</application>
+		<application>sidock</application>
 		<stdout_filename>docking_log</stdout_filename>
 		<command_line>-c -j 1 -b 1 -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
 		<checkpoint_filename>docking_out.chk</checkpoint_filename>
diff --git a/sci-biology/cmdock/metadata.xml b/sci-biology/cmdock/metadata.xml
index 3a84323920..234b93fc4c 100644
--- a/sci-biology/cmdock/metadata.xml
+++ b/sci-biology/cmdock/metadata.xml
@@ -7,7 +7,7 @@
 	</maintainer>	
 	<upstream>
 		<remote-id type="gitlab">Jukic/cmdock</remote-id>
-		<bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to>
+		<bugs-to>https://gitlab.com/Jukic/cmdock/-/work_items</bugs-to>
 		<doc>https://rxdock.gitlab.io/documentation/devel/html/</doc>
 	</upstream>
 	<use>