Finish incorporating Gilson edits to references as well as my own.

Author: davidlmobley

paper/benchmarkset.bib

@@ -756,15 +756,18 @@ @article{merski_homologous_2015
 
 @article{lim_sensitivity_2016,
   title = {Sensitivity in Binding Free Energies due to Protein Reorganization},
+  volume = {12},
   issn = {1549-9618, 1549-9626},
   doi = {10.1021/acs.jctc.6b00532},
   language = {en},
-  timestamp = {2016-08-15T18:43:59Z},
+  timestamp = {2016-12-08T23:08:28Z},
+  number = {9},
   urldate = {2016-08-15},
   journal = {Journal of Chemical Theory and Computation},
   author = {Lim, Nathan M. and Wang, Lingle and Abel, Robert and Mobley, David L},
   month = jul,
   year = {2016},
+  pages = {4620--4631},
   file = {acs%2Ejctc%2E6b00532.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SVUZNG5Q/acs%2Ejctc%2E6b00532.pdf:application/pdf}
 }
 
@@ -2440,29 +2443,29 @@ @article{hajduk_statistical_2008
 }
 
 @misc{christ_binding_2016,
-  address = {Boston, MA},
   title = {Binding Affinity Prediction from Molecular Simulations: {{A}} New Standard Method in Structure-Based Drug Design?},
-  timestamp = {2016-09-02T16:06:32Z},
+  timestamp = {2016-12-08T23:06:46Z},
+  howpublished = {\url{dx.doi.org/10.7490/f1000research.1112651.1}},
   author = {Christ, Clara D.},
   month = may,
   year = {2016},
   file = {f1000research-130266.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5ZIS5B5E/f1000research-130266.pdf:application/pdf}
 }
 
 @misc{cui_affinity_2016,
-  address = {Boston, MA},
   title = {Affinity {{Predictions}} with {{FEP}}+: {{A Different Perspective}} on {{Performance}} and {{Utility}}},
-  timestamp = {2016-09-02T16:12:43Z},
+  timestamp = {2016-12-08T23:06:55Z},
+  howpublished = {\url{dx.doi.org/10.7490/f1000research.1112773.1}},
   author = {Cui, Guanglei},
   month = may,
   year = {2016},
   file = {f1000research-131922.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SBUX9HUR/f1000research-131922.pdf:application/pdf}
 }
 
 @misc{verras_free_2016,
-  address = {Boston, MA},
   title = {Free {{Energy Perturbation}} at {{Merck}}: {{Benchmarking}} against {{Faster Methods}}},
-  timestamp = {2016-09-02T16:11:50Z},
+  timestamp = {2016-12-08T23:07:14Z},
+  howpublished = {\url{http://www.alchemistry.org/wiki/images/c/c3/Vertex_FreeEnergyWorkshop2016_AV.pdf}},
   author = {Verras, Andreas},
   month = may,
   year = {2016},
@@ -3872,6 +3875,26 @@ @incollection{Fromming:1994:CyclodextrinsinPharmacy
   pages = {19--32}
 }
 
+@article{Gilson:2016:Nucl.AcidsRes.,
+  title = {{{BindingDB}} in 2015: {{A}} Public Database for Medicinal Chemistry, Computational Chemistry and Systems Pharmacology},
+  volume = {44},
+  issn = {0305-1048, 1362-4962},
+  shorttitle = {{{BindingDB}} in 2015},
+  doi = {10.1093/nar/gkv1072},
+  abstract = {BindingDB, www.bindingdb.org, is a publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US patents. BindingDB provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. The PDB and PubMed provide links to data in BindingDB, and vice versa; and BindingDB provides links to pathway information, the ZINC catalog of available compounds, and other resources. The BindingDB website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. Specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from BindingDB and organized for use in validating drug design methods. BindingDB offers several forms of programmatic access, and comes with extensive background material and documentation. Here, we provide the first update of BindingDB since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole.},
+  language = {en},
+  timestamp = {2016-12-08T22:45:13Z},
+  number = {D1},
+  urldate = {2016-12-08},
+  journal = {Nucl. Acids Res.},
+  author = {Gilson, Michael K. and Liu, Tiqing and Baitaluk, Michael and Nicola, George and Hwang, Linda and Chong, Jenny},
+  month = apr,
+  year = {2016},
+  pages = {D1045--D1053},
+  file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/X65QJVGV/Gilson et al. - 2016 - BindingDB in 2015 A public database for medicinal.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/QSEKC6IN/D1045.html:text/html},
+  pmid = {26481362}
+}
+
 @comment{jabref-meta: groupsversion:3;}
 @comment{jabref-meta: groupstree:
 0 AllEntriesGroup:;

paper/benchmarkset.pdf

@@ -780,8 +780,7 @@ \subsubsection{Bromodomain proteins}
 Docking calculations included in the same study did not work as well.
 The compounds studied were diverse, and therefore not amenable to relative free energy methods in which one ligand is computationally converted into another. 
 Overall, then, this appears to be class of systems that could yield relatively tractable and informative protein-ligand benchmark systems. 
-One known challenge is that some ligands have multiple plausible binding modes \cite{?}. 
-%DLM: Add cite
+One known challenge is that some ligands have multiple plausible binding modes \cite{aldeghi_accurate_2016}. 
  In addition, a diverse ligand series can pose severe challenges for relative free energy techniques.