diff --git a/src/isdb/CS2Backbone.cpp b/src/isdb/CS2Backbone.cpp
index 2970b6ff36e68912ea0ee72a34d41908f192cf66..73d309c41c56701e949a583061d704d864521033 100644
--- a/src/isdb/CS2Backbone.cpp
+++ b/src/isdb/CS2Backbone.cpp
@@ -37,8 +37,6 @@
 
 #include "MetainferenceBase.h"
 #include "core/ActionRegister.h"
-#include "core/PlumedMain.h"
-#include "tools/OpenMP.h"
 #include "tools/Pbc.h"
 #include "tools/PDB.h"
 #include "tools/Torsion.h"
@@ -658,6 +656,7 @@ CS2Backbone::CS2Backbone(const ActionOptions&ao):
      <<plumed.cite("Kohlhoff K, Robustelli P, Cavalli A, Salvatella A, Vendruscolo M, J. Am. Chem. Soc. 131, 13894 (2009)");
   if(camshift) log<<plumed.cite("Granata D, Camilloni C, Vendruscolo M, Laio A, Proc. Natl. Acad. Sci. USA 110, 6817 (2013)");
   else log<<plumed.cite("Camilloni C, Robustelli P, De Simone A, Cavalli A, Vendruscolo M, J. Am. Chem. Soc. 134, 3968 (2012)");
+  log<<plumed.cite("Bonomi M, Camilloni C, Bioinformatics, 33, 3999 (2017)");
   log<<"\n";
 
   const string str_cs[] = {"ha_","hn_","nh_","ca_","cb_","co_"};
diff --git a/src/isdb/EMMI.cpp b/src/isdb/EMMI.cpp
index 313287ab108ee22a80d1afbe1fe96dc78b72cb41..5c49e5e9a7925eae5fa3c8fa7f792e7aba88b91c 100644
--- a/src/isdb/EMMI.cpp
+++ b/src/isdb/EMMI.cpp
@@ -336,6 +336,7 @@ EMMI::EMMI(const ActionOptions&ao):
 
   log<<"  Bibliography "<<plumed.cite("Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)");
   log<<plumed.cite("Hanot, Bonomi, Greenberg, Sali, Nilges, Vendruscolo, Pellarin, bioRxiv doi: 10.1101/113951 (2017)");
+  log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
   log<<"\n";
 }
 
diff --git a/src/isdb/FretEfficiency.cpp b/src/isdb/FretEfficiency.cpp
index 079ee9b7a64efd91be88bb31e8da3bd02d2a13a4..28dc4f6762cae79130adb60d23c8d68b619e1e83 100644
--- a/src/isdb/FretEfficiency.cpp
+++ b/src/isdb/FretEfficiency.cpp
@@ -21,6 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "colvar/Colvar.h"
 #include "colvar/ActionRegister.h"
+#include "core/PlumedMain.h"
 #include "tools/Pbc.h"
 
 #include <string>
@@ -118,6 +119,8 @@ FretEfficiency::FretEfficiency(const ActionOptions&ao):
 
   if(pbc) log.printf("  using periodic boundary conditions\n");
   else    log.printf("  without periodic boundary conditions\n");
+  
+  log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
 
   addValueWithDerivatives();
   setNotPeriodic();
diff --git a/src/isdb/Jcoupling.cpp b/src/isdb/Jcoupling.cpp
index bb0651e5f9edfe41d05b9125738022e27f995c8d..c335a50eae0d527873cbb9f557c1c82f49cb132c 100644
--- a/src/isdb/Jcoupling.cpp
+++ b/src/isdb/Jcoupling.cpp
@@ -21,8 +21,6 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "MetainferenceBase.h"
 #include "core/ActionRegister.h"
-#include "core/PlumedMain.h"
-#include "tools/OpenMP.h"
 #include "tools/Pbc.h"
 #include "tools/Torsion.h"
 
@@ -212,6 +210,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
     parse("SHIFT", kshift_);
   }
 
+  log << "  Bibliography ";
 
   // Set Karplus parameters
   switch (jtype_) {
@@ -221,8 +220,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
     kc_ = -0.27;
     kshift_ = pi / 3.0;
     log.printf("J-coupling type is HAN, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
-    log << "  Bibliography "
-        << plumed.cite("Wang A C, Bax A, J. Am. Chem. Soc. 117, 1810 (1995)") << "\n";
+    log << plumed.cite("Wang A C, Bax A, J. Am. Chem. Soc. 117, 1810 (1995)");
     break;
   case HAHN:
     ka_ = 7.09;
@@ -230,8 +228,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
     kc_ = 1.55;
     kshift_ = -pi / 3.0;
     log.printf("J-coupling type is HAHN, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
-    log << "  Bibliography "
-        << plumed.cite("Hu J-S, Bax A, J. Am. Chem. Soc. 119, 6360 (1997)") << "\n";
+    log << plumed.cite("Hu J-S, Bax A, J. Am. Chem. Soc. 119, 6360 (1997)");
     break;
   case CCG:
     ka_ = 2.31;
@@ -239,8 +236,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
     kc_ = 0.55;
     kshift_ = (2.0 * pi) / 3.0;
     log.printf("J-coupling type is CCG, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
-    log << "  Bibliography "
-        << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)") << "\n";
+    log << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)");
     break;
   case NCG:
     ka_ = 1.29;
@@ -248,13 +244,14 @@ JCoupling::JCoupling(const ActionOptions&ao):
     kc_ = 0.37;
     kshift_ = 0.0;
     log.printf("J-coupling type is NCG, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
-    log << "  Bibliography "
-        << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)") << "\n";
+    log << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)");
     break;
   case CUSTOM:
     log.printf("J-coupling type is custom, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
     break;
   }
+  log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
+  log<<"\n";
 
   for (unsigned i = 0; i < ncoupl_; ++i) {
     log.printf("  The %uth J-Coupling is calculated from atoms : %d %d %d %d.",
diff --git a/src/isdb/Metainference.cpp b/src/isdb/Metainference.cpp
index 5bdf32c131e0ce2c5dd3449855ee689667aa7b4a..2536c0f50f6295da04275a7d34ac65713301cb6c 100644
--- a/src/isdb/Metainference.cpp
+++ b/src/isdb/Metainference.cpp
@@ -752,6 +752,7 @@ Metainference::Metainference(const ActionOptions&ao):
   log<<"  Bibliography "<<plumed.cite("Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)");
   if(do_reweight_) log<<plumed.cite("Bonomi, Camilloni, Vendruscolo, Sci. Rep. 6, 31232 (2016)");
   if(do_optsigmamean_>0) log<<plumed.cite("Loehr, Jussupow, Camilloni, J. Chem. Phys. 146, 165102 (2017)");
+  log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
   log<<"\n";
 }
 
diff --git a/src/isdb/MetainferenceBase.cpp b/src/isdb/MetainferenceBase.cpp
index c192a199cf807161d451ed5fe78f895f42d02b5f..381fa96b34f35c9004b0b3ea9230ae63c35a1af8 100644
--- a/src/isdb/MetainferenceBase.cpp
+++ b/src/isdb/MetainferenceBase.cpp
@@ -20,9 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "MetainferenceBase.h"
-#include "core/PlumedMain.h"
 #include "tools/File.h"
-#include "tools/OpenMP.h"
 #include <cmath>
 #include <ctime>
 #include <numeric>
@@ -552,6 +550,7 @@ void MetainferenceBase::Initialise(const unsigned input)
   log<<"  Bibliography "<<plumed.cite("Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)");
   if(do_reweight_) log<<plumed.cite("Bonomi, Camilloni, Vendruscolo, Sci. Rep. 6, 31232 (2016)");
   if(do_optsigmamean_>0) log<<plumed.cite("Loehr, Jussupow, Camilloni, J. Chem. Phys. 146, 165102 (2017)");
+  log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
   log<<"\n";
 }
 
diff --git a/src/isdb/MetainferenceBase.h b/src/isdb/MetainferenceBase.h
index 5fc1affa84dbc9efead5b8bb2cb060f0df243bc7..7594d2b98dca99d21b3a608df54b7c0d254620e3 100644
--- a/src/isdb/MetainferenceBase.h
+++ b/src/isdb/MetainferenceBase.h
@@ -25,7 +25,9 @@
 #include "core/ActionWithValue.h"
 #include "core/ActionAtomistic.h"
 #include "core/ActionWithArguments.h"
+#include "core/PlumedMain.h"
 #include "tools/Random.h"
+#include "tools/OpenMP.h"
 
 #define PLUMED_METAINF_INIT(ao) Action(ao),MetainferenceBase(ao)
 
diff --git a/src/isdb/NOE.cpp b/src/isdb/NOE.cpp
index ec130d9df8a9e390586b2004e7ce643f3f139d01..64b53e8a6a16e30d78e01a1cf1a208236f0a391e 100644
--- a/src/isdb/NOE.cpp
+++ b/src/isdb/NOE.cpp
@@ -22,7 +22,6 @@
 #include "MetainferenceBase.h"
 #include "core/ActionRegister.h"
 #include "tools/NeighborList.h"
-#include "tools/OpenMP.h"
 #include "tools/Pbc.h"
 
 #include <string>
@@ -165,6 +164,8 @@ NOE::NOE(const ActionOptions&ao):
   if(pbc)      log.printf("  using periodic boundary conditions\n");
   else         log.printf("  without periodic boundary conditions\n");
 
+  log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
   if(!getDoScore()) {
     for(unsigned i=0; i<nga.size(); i++) {
       string num; Tools::convert(i,num);
diff --git a/src/isdb/PRE.cpp b/src/isdb/PRE.cpp
index 83702f1d73e676e9c01bd52cb94c532e5f6051c5..6b9a38febe5e78dc96baec8eb316ba3f75ade1a6 100644
--- a/src/isdb/PRE.cpp
+++ b/src/isdb/PRE.cpp
@@ -22,7 +22,6 @@
 #include "MetainferenceBase.h"
 #include "core/ActionRegister.h"
 #include "tools/NeighborList.h"
-#include "tools/OpenMP.h"
 #include "tools/Pbc.h"
 
 #include <string>
@@ -205,6 +204,8 @@ PRE::PRE(const ActionOptions&ao):
   if(pbc)      log.printf("  using periodic boundary conditions\n");
   else         log.printf("  without periodic boundary conditions\n");
 
+  log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
   if(!getDoScore()) {
     for(unsigned i=0; i<nga.size(); i++) {
       string num; Tools::convert(i,num);
diff --git a/src/isdb/RDC.cpp b/src/isdb/RDC.cpp
index c871c3800ec2d0f822757bed19879c216524cc3d..a0be6cf1992674aaf188e64c3a6b4e05aac974d5 100644
--- a/src/isdb/RDC.cpp
+++ b/src/isdb/RDC.cpp
@@ -21,8 +21,6 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "MetainferenceBase.h"
 #include "core/ActionRegister.h"
-#include "core/PlumedMain.h"
-#include "tools/OpenMP.h"
 #include "tools/Pbc.h"
 
 #ifdef __PLUMED_HAS_GSL
@@ -287,7 +285,9 @@ RDC::RDC(const ActionOptions&ao):
 
   log<<"  Bibliography "
      <<plumed.cite("Camilloni C, Vendruscolo M, J. Phys. Chem. B 119, 653 (2015)")
-     <<plumed.cite("Camilloni C, Vendruscolo M, Biochemistry 54, 7470 (2015)") <<"\n";
+     <<plumed.cite("Camilloni C, Vendruscolo M, Biochemistry 54, 7470 (2015)");
+  log<< plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
 
   if(!getDoScore()&&!svd) {
     for(unsigned i=0; i<ndata; i++) {
diff --git a/src/isdb/Rescale.cpp b/src/isdb/Rescale.cpp
index 3707c1c2217c8e4ee1124f2fe35e33d900702da0..f28dce8b53106f3b4a384c16f6c5e9fb53cea03d 100644
--- a/src/isdb/Rescale.cpp
+++ b/src/isdb/Rescale.cpp
@@ -288,6 +288,9 @@ Rescale::Rescale(const ActionOptions&ao):
   log.printf("  do MC every %d steps\n", MCstride_);
   log.printf("\n");
 
+  log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
+
   // add components
   addComponent("igamma");   componentIsNotPeriodic("igamma");
   addComponent("accgamma"); componentIsNotPeriodic("accgamma");
diff --git a/src/isdb/SAXS.cpp b/src/isdb/SAXS.cpp
index 3f5ab61dcfc856521d64ccaf423901a9233950d8..2e965236b7b723c4634b689317a0138553b7b50d 100644
--- a/src/isdb/SAXS.cpp
+++ b/src/isdb/SAXS.cpp
@@ -27,10 +27,8 @@
 #include "MetainferenceBase.h"
 #include "core/ActionRegister.h"
 #include "core/ActionSet.h"
-#include "core/PlumedMain.h"
 #include "core/SetupMolInfo.h"
 #include "tools/Communicator.h"
-#include "tools/OpenMP.h"
 #include "tools/Pbc.h"
 
 #include <string>
@@ -277,6 +275,7 @@ SAXS::SAXS(const ActionOptions&ao):
     log<<plumed.cite("Fraser, MacRae, Suzuki, J. Appl. Crystallogr., 11, 693–694 (1978).");
     log<<plumed.cite("Brown, Fox, Maslen, O'Keefe, Willis, International Tables for Crystallography C, 554–595 (International Union of Crystallography, 2006).");
   }
+  log<< plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
   log<<"\n";
 
   requestAtoms(atoms);
diff --git a/src/isdb/Select.cpp b/src/isdb/Select.cpp
index de6f0ae4b11fd99e3d185df411faa66242d64c46..14368243a5f7f1540deecd7350560e758e78238a 100644
--- a/src/isdb/Select.cpp
+++ b/src/isdb/Select.cpp
@@ -95,6 +95,8 @@ Select::Select(const ActionOptions&ao):
   checkRead();
 
   log.printf("  select based on %s\n",selector_.c_str());
+  log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
 }
 
 void Select::calculate()
diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib
index 2ad2f9abcac3cc5a5e0fe1798826055d183a64c3..e4ca5b0eba03377dd2365275d966d82802380e02 100644
--- a/user-doc/bibliography.bib
+++ b/user-doc/bibliography.bib
@@ -2569,8 +2569,8 @@ author = {Bonomi, Massimiliano and Camilloni, Carlo},
 title = {{Integrative structural and dynamical biology with PLUMED-ISDB}},
 journal = {Bioinformatics},
 year = {2017},
-volume = {},
-pages = {},
+volume = {33},
+pages = {3999--4000},
 }
 
 @Article{Lelievre2007,