diff --git a/sci-chemistry/tm-align/files/CMakeLists.txt b/sci-chemistry/tm-align/files/CMakeLists.txt
index 506ef136309e4..64507389838b5 100644
--- a/sci-chemistry/tm-align/files/CMakeLists.txt
+++ b/sci-chemistry/tm-align/files/CMakeLists.txt
@@ -1,6 +1,9 @@
-cmake_minimum_required (VERSION 2.6)
+cmake_minimum_required (VERSION 3.28)
 project (TMTools Fortran)
+
+include(GNUInstallDirs)
+
 add_executable(TMalign TMalign.f)
 add_executable(TMscore TMscore.f)
 
-install (TARGETS TMalign TMscore DESTINATION bin)
+install (TARGETS TMalign TMscore DESTINATION ${CMAKE_INSTALL_BINDIR})
diff --git a/sci-chemistry/tm-align/tm-align-20150914-r1.ebuild b/sci-chemistry/tm-align/tm-align-20150914-r1.ebuild
index 800884db81388..1dd858d1b60e5 100644
--- a/sci-chemistry/tm-align/tm-align-20150914-r1.ebuild
+++ b/sci-chemistry/tm-align/tm-align-20150914-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -8,13 +8,22 @@ inherit cmake flag-o-matic fortran-2
 DESCRIPTION="Quick & Accurate Structural Alignment"
 HOMEPAGE="https://zhanggroup.org/TM-align/"
 SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz"
-S="${WORKDIR}"
 
 LICENSE="tm-align"
 SLOT="0"
 KEYWORDS="amd64 ~ppc ppc64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="custom-cflags"
 
+BDEPEND=">=dev-build/cmake-3.28"
+
+src_unpack() {
+	# S=${WORKDIR} is deprecated in cmake eclass
+	mkdir "${P}" || die
+	pushd "${P}" || die
+		unpack ${A}
+	popd || die
+}
+
 src_prepare() {
 	cp "${FILESDIR}"/CMakeLists.txt . || die
 	cmake_src_prepare