239
Genome Informatics 17(2): 239{247 (2006)
A Large-Scale Computational Approach to Drug
Repositioning
Yvonne Y. Li
Jianghong An
yli@bcgsc.ca
jan@bcgsc.ca
Steven J.M. Jones
sjones@bcgsc.ca
Canada's Michael Smith Genome Sciences Centre, 570 West 7th Avenue, Vancouver,
British Columbia, V5Z 4S6, Canada
Abstract
We have developed a computational pipeline for the prediction of protein-small molecule interactions and have applied it to the drug repositioning problem through a large-scale analysis of
known drug targets and small molecule drugs. Our pipeline combines forward and inverse docking,
the latter of which is a twist on the conventional docking procedure used in drug discovery: instead
of docking many compounds against a speci c target to look for potential inhibitors, one compound
is docked against many proteins to search for potential targets. We collected an extensive set of
1,055 approved small molecule drugs and 1,548 drug target binding pockets (representing 78 unique
human protein therapeutic targets) and performed a large-scale docking using ICM software to both
validate our method and predict novel protein-drug interactions. For the 37 known protein-drug
interactions in our data set that have a known structure complex, all docked conformations were
within 2.0
A of the solved conformation, and 30 of these had a docking score passing the typical
ICM score threshold. Out of the 237 known protein-drug interactions annotated by DrugBank,
74 passed the score threshold, and 52 showed the drug docking to another protein with a better
docking score than to its known target. These protein targets are implicated in human diseases, so
novel protein-drug interactions discovered represent potential novel indications for the drugs. Our
results highlight the promising nature of the inverse docking method for identifying potential novel
therapeutic uses for existing drugs.
Keywords:
drug repositioning, computational drug discovery, inverse docking, docking
1 Introduction
An integral part of recent computational drug discovery research focuses on the high-throughput
screening of chemical databases to nd inhibitors of speci c protein targets. However, drugs designed
to interact speci cally with a certain target frequently also interact with other proteins. These o target interactions may cause harmful drug side e ects; however, they may also lead to new therapeutic
opportunities. Understanding the potential o -target interactions of existing drugs is of major interest
to pharmaceutical research, not only for providing insight into drug side e ects, but also for discovering
novel therapeutic uses of drugs. Finding new indications for existing drugs, also known as drug
repositioning, represents an ecient approach to drug discovery, since existing drugs already have
clinical history and thus require much less time and money to develop into a drug speci c for the new
disease [3].
Molecular docking is a computational method used to predict how a ligand molecule interacts with
a protein binding site, both in terms of binding conformation and binding anity. This method is
well established as a virtual screening method in drug discovery [13], where typically a large compound database is docked against a speci c protein binding site, in order to discover novel inhibitors
Li et al.
240
of that target. The inverse scenario, whereby a speci c small molecule is docked to a panel of protein targets - so called `inverse docking' - has been little studied. This method was rst used by
Chen and Zhi [9] in 2001 to predict potential o -target protein-drug interactions. Since then, a few
studies have used it for predicting unanticipated kinase targets of several kinase inhibitors [17]. The
combination of forward and inverse docking has been used in cross-docking studies for investigating
enzyme-metabolite selectivity [15] and used in creating protein-ligand docking anity matrices for
improving the enrichment factor of virtual screening [11].
However, inverse docking is also suited to computational drug repositioning analysis. By docking
an existing drug to a panel of known therapeutic targets, the potential of the drug to bind targets
other than its intended can be assessed, thus leading to potential drug therapies for other diseases.
Such a method would be particularly valuable for improving the eciency of current drug discovery
pipelines. Here, we present a computational approach that combines forward and inverse docking for
the drug repositioning problem.
✘✘✙
✙
✝
✚
✛
✜✠✠✂✁✂✝
✁✡✛
✍✗✔✒✜✎✍✂✄✡✔✑☞☎✒✎✂✓✠✏✂☎✒✝
✌
✁☞✎✍✄✖✁✂✔✔✡✡✑✄✕✕☛☞☎☎✒✗✆✒✎✂✍✓
✆☎☞✚
✞
✟
✄✄✢
☎
☞✔☞✖✕✒☎✡✍✁☛✄✤✡✁☛✏✝
✏
☎☞✡✕✠✁✔✄✂✏✠✏✌
✡
☛
☞✣
✧
✚
✛
✝
✂☛✒✎✄✍✓✦✡✆☞✁☎
✜✥
2 Method and Results
2.1
Molecular Docking Pipeline
The automated molecular docking pipeline was implemented using the ICM software package [1] and
is illustrated in Figure 1.
Figure 1: The molecular docking pipeline.
Given a list of Protein Data Bank (PDB) identi ers, the protein 3D structures are retrieved from
PDB and are rst required to be X-ray crystal structures with a minimum resolution of 2.5
A. The
structures are then separated into chains as annotated in PDB. For structures with multiple chains, its
chains are grouped into a set of non-redundant sequences, based on PDB's chain redundancy analysis
at the 95% sequence identity level [5].
The PDB structures are prepared for docking by adding and optimizing hydrogens and by removing
water molecules, metal ions, and other solvent molecules. Pockets are predicted in the structures using
the PocketFinder algorithm, which is based on a transformation of the van der Waals potential [2]. This
algorithm has been shown to have excellent predictive capability for human pockets: when applied to
a large and comprehensive data set of 17,126 human protein pockets, PocketFinder correctly predicted
96.8% of holo pockets and 95% of apo pockets [2].
Predicted pockets are then further ltered for quality. First, they are de ned at a cut-o of
minimum 150
A3 volume. Second, when multiple pockets are predicted in a protein, the two largest
A Large-Scale Computational Approach to Drug Repositioning
241
are retained. Though this will inevitably omit real druggable sites, the PocketFinder method has
shown that its two largest predicted pockets may cover as many as 92.7% of real binding sites [2].
Third, pockets that have residues within 3.5
A with occupancy values less than 1 or temperature factors
(B-factors) greater than 60 are removed - these are non-stringent cut-o s used only to detect the most
unreliable residues. Finally, the protein's observed PDB sequence is aligned to its known SwissProt
sequence and pockets that have residues within 3.5
A which are engineered mutations or missing in
the observed sequence are removed. An example of predicted pockets for the Hemoglobin alpha chain
protein is shown in Figure 2. For each pocket, the receptor is de ned as a box with a 3.5
A margin
around the outermost points of the pocket.
The small molecule database is prepared as a multi-object sdf le and docked to each pocket. ICM
performs grid-based rigid-receptor exible-ligand docking through a modi ed Monte-Carlo searching
procedure and a rigorous empirical scoring function. ICM has performed well in recent assessments
of popular docking packages (including, Glide, GOLD, Autodock, DOCK) [6, 8], and has shown topranking pose prediction accuracies of 45% [16] and 50% [8] in studies using small protein benchmark
sets. After docking, the scores and conformations of high scoring compounds are gathered for further
analysis. For proteins with multiple pockets, the docking score of the best scoring pocket is used to
represent the protein-small molecule interaction. These time-intensive pocket prediction, preparation,
and docking steps are rendered feasible by using a 400-processor cluster, on which we have ICM
licensed for 200 processors.
2.2
Data Set: Binding Pocket Database and Small Molecule Drug Database
We drew known protein-drug interactions from DrugBank [18], a manually curated database holding
detailed information on drugs and protein targets. DrugBank contains therapeutically useful interactions for over 4,000 drugs, including FDA-approved, experimental, biotech, and nutriceutical drugs,
corresponding to over 6,000 drug targets. For our analysis, we rst focused on the 1,055 FDA approved
drugs and their corresponding 510 human proteins targets.
447 SwissProt identi ers of therapeutic targets corresponding to 1,055 known small molecule drugs
were retrieved from DrugBank. 1,345 X-ray PDB structures with resolution better than 2.5
A were
obtained for 165 of these proteins for which 246 known drugs corresponded. This resulted in 1,836 nonredundant PDB chains with at least one chain per structure. PocketFinder predicted 2,272 pockets
when the two largest pockets over 150
A3 were retained. After the B-factor and occupancy ltering
step, 2,082 pockets remained. After removing pockets with nearby engineered mutations or gaps,
1,548 pockets remained, representing 78 unique human proteins.
The 1,055 approved small molecule drugs with sdf representation were downloaded from DrugBank.
Known protein-drug interactions used to assess docking results were obtained from DrugBank's Approved DrugCards ( le dated 2005/6/27). 237 of them are represented by proteins and drugs in our
data set.
2.3
Re-Docking Known Protein-Drug Complexes
Of the 237 known protein-drug interactions in the data set, 37 interactions (representing 19 unique
proteins) have already been solved in a PDB structure complex. We rst veri ed whether these
interactions could be predicted using our pipeline. The advantage of this benchmark data set is that
both the binding site and binding conformations for the ligand are known. We docked cognate ligands
to predicted protein pockets for these 37 interactions. For this smaller data set, we performed a more
rigorous pocket prediction in that pockets containing metal ions were prepared with the metal ion
present. In addition, for multi-chain proteins, we also predicted inter-chain pockets (one example is
shown in Figure 2). There were 101 pockets in total.
The results are summarized in Table 1, listing for each interaction the docking score and the root
mean square deviation (RMSD) value between the docked ligand and the PDB conformation. All 37
Li et al.
242
Figure 2: Left: The two pockets predicted for PDB entry 1R1X (Hemoglobin alpha chain) overlap
well with known ligand positions. Right: The binding pocket (darker glob) of PDB entry 1TCO is
comprised of three separately colored chains.
complexes exhibit a RMSD value less than 2.0
A which is the standard cuto used to de ne a successful
molecular docking. 31 of the 37 complexes exhibit an RMSD value less than 1.0
A which is a much more
rigorous measure of successful docking [8]. A couple of docked examples in Figure 3 illustrate that even
large exible ligands are docked correctly. The low RMSD values also show that despite retaining two
pockets for each protein, the best scoring ligand conformation always docked to the correct pocket.
However, though the RMSDs were all well predicted, docking scores in only 29 of the 37 complexes
were smaller (better) than the default ICM score cuto (which is -32). Further investigation shows
the poorly scoring complexes all involve pockets with a metal ion present. It should be noted that
we also tried docking without the metal in the pocket, and though the scores were more reasonable
(around -25), the RMSDs were greater than 2.0
A. Thus it seems, at the moment, we are not able to
predict reliable scores for pockets containing metals.
Overall, these results show that the docking and scoring algorithms are quite accurate predictors
of actual protein-drug binding when the protein is already in a correct conformation.
Table 1: Docking score and RMSD values for the re-docking of the 37 structure complexes.
PDB PDB RMSD Dock PDB PDB RMSD Dock PDB PDB RMSD Dock
protein ligand (
A) score protein ligand (
A) score protein ligand (
A) score
1K74
REA
0.8
-71.0
1BRP
RTL
0.5
-48.7
1UHO
VDN
1.3
-35.7
1FM6
REA
0.4
-70.1
3ERD
DES
0.3
-48.4
1FKJ
FK5
0.8
-35.5
1FM9
REA
0.5
-69.7
1SQN
NDR
0.4
-45.9
1BKF
FK5
0.9
-35.1
1FBY
REA
0.6
-67.9
1HWI
MMM2
0.5
-45.7
1MMK
BH4
0.4
-33.1
1XZX
T3
0.5
-60.6
1RBP
MMM2
0.7
-58.8
1Z95
2LBD
REA
0.4
-58.0
1XP0
1T46
STI
0.4
-56.4
1HWK
RTL
0.4
-44.0
1KW0
BH4
0.5
-29.8
0.4
-42.8
1XOZ
CIA
0.7
-25.1
VDN
1.3
-39.6
1XLX
CIO
1.5
-19.4
1FKB
RAP
0.7
-39.6
1UZF
0.5
-14.9
MMMM
AMCO
3LBD
REA
0.4
-55.9
1NB9
RBF
0.8
-39.0
1J8U
THB
1.7
-12.5
1HWJ
MMM2
0.4
-54.7
1TBF
VIA
0.8
-38.9
1CIL
ETS
0.6
-9.9
1TCO
FK5
0.8
-52.9
1FKF
FK5
0.7
-36.7
1A42
BZO
1.7
-7.7
1A28
ASTR
0.3
-50.4
1HWL
FBI
0.5
-36.0
1AZM
AZM
1.4
-7.7
1M2Z
DEX
0.4
-49.4
A Large-Scale Computational Approach to Drug Repositioning
243
Figure 3: Left: 1HWK (HMDH HUMAN) is shown with complexed ligand Atorvastatin and its docked
conformation. Right: The ligand Alitretinoin of 2LBD (RARG2 HUMAN) is shown in its predicted
pocket along with the docked conformation.
2.4
Large-Scale Docking
A large scale docking using ICM was carried out for the 1,055 approved drugs against the 1,548
pockets. Proteins represented by multiple PDB structures (i.e. multiple pockets) use the best scoring
drug-pocket interaction as the protein-drug docking score. Results are illustrated in Figure 4 with the
1,055 drugs along the horizontal and 31 of the 78 proteins along the vertical.
Though ICM recommends a docking score cut-o of -32, this value should ideally be tailored to
each receptor. For example, a study using ICM docking to EGFR discovered novel inhibitors with a
cut-o value of -28 [7]. We chose to apply a simple receptor-speci c threshold system. For proteins
belonging to the 37 known complexes in the re-docking analysis, we used those docking scores as
cut-o s. If protein is known to bind several drugs, as is often the case in our data set, the cut-o
was the poorest known-drug-score (but still better than the default -32). These cut-o s are the most
reliable since it is known that the drug docked to the correct binding site with a correct conformation.
For proteins that are not in a known structure complex but showed a good docking score (better than
-32) with a known interacting drug, we used this docking score as the cut-o . These cut-o s are less
reliable since without a 3D structure, we cannot be absolutely sure that the drug docked to the correct
protein pocket with a correct conformation. The remaining 47 proteins of the 78 did not have any
known interactions predicted with a good score and are not shown in Figure 4.
Of the 237 known protein-drug interactions, 74 show a docking score better than -32. In such cases,
it is interesting to examine how a protein ranks when the drug is docked to all proteins (`ProteinRank'
or inverse docking rank) as well as how the drug ranks when all drugs are docked to the protein
(`DrugRank' or docking rank). Thus, ProteinRank ranges from 1 to 78 whereas DrugRank ranges
from 1 to 1,055. The ranks for a few of the 74 good-scoring known interactions are shown in Table 2,
illustrating several di erent rank combinations.
When both ranks are high, the protein and drug are speci c to each other. A ProteinRank that is
not 1 suggests that the drug may bind to another target as well as the primary target. A DrugRank
that is not 1 suggests that other drugs may have potential to bind this protein. In total, 52 of the
74 interactions do not have a ProteinRank of 1, and are thus interesting for further investigation.
Li et al.
244
Figure 4: Map of large-scale docking results, with speci c scoring thresholds applied for each protein.
The 1,055 drugs are represented on the horizontal and the 31 proteins having a good docking score
with a known drug are on the vertical. Protein-drug interactions whose docking score does not surpass
their designated cut-o are shown as black and those that do are shown in gray (where brighter shades
of gray represent better scores).
For example, in the case of Acitretin and Retinoic acid receptor gamma-1 (RARG1 HUMAN) for
treatment of severe adult psoriasis, some top targets for Acitretin are shown in Table 3. DrugBank
annotated 7 targets, 2 of which do not have a solved human structure, leaving 5 targets in our input
data set. All ve targets (shaded rows) show good docking scores with this drug, despite that there
are no solved structures of this drug in complex with any protein. The top ranking target is serum
albumin, and though it was not annotated in DrugBank as a drug target, it was noted that in the
systemic circulation, over 98% of Acitretin is bound to lipoproteins or albumin in the blood [10]. The
remaining targets are novel potential targets of this drug, and should be the rst to be experimentally
tested for a laboratory interested in Acitretin repositioning. In Table 2, it can be seen that Acitretin
is the 9th ranked drug for RARG1 HUMAN. There are thus 8 other known drugs that have potential
to be repositioned for severe psoriasis.
Table 2: The ProteinRank and DrugRank for several known protein-drug interactions. Proteins are
denoted by their SwissProt identi ers.
Protein
Drug
RARG1 HUMAN
Alitretinoin
KIT HUMAN
Imatinib
PRGR HUMAN Medroxyprogesterone
RETBP HUMAN
Vitamin A
RARG1 HUMAN
Acitretin
ICM Score Protein Rank Drug Rank
-59.1
-49.0
-47.8
-52.6
-46.3
1
1
1
3
2
1
1
14
1
9
When both ranks are 1, there is no drug in the database that docks better to the protein target,
and there is no other protein to which the drug docks better. This means that the protein-drug
combination is ideal within the scope of the data set, and no better target can be found for the drug.
This situation may still be interesting for drug repositioning in two scenarios: rst, if more proteins
are included in the data set, the rankings may change; second, ICM docking does not purport to rank
results by binding anity - thus, docking scores lower than a known interaction (though they should
still be close to or better than the default -32 score) may also re ect potential binding interactions.
For example, imatinib is a well-known inhibitor of the Bcr-Abl fusion protein for the treatment of
chronic myeloid leukemia. In our docking analysis, the ABL-imatinib interaction was docked with a
score of -31.6, not passing the score threshold. However, closer inspection of the human ABL structure,
A Large-Scale Computational Approach to Drug Repositioning
245
Table 3: Inverse docking results for Acitretin. Proteins are denoted by their SwissProt identi ers.
Known targets are shaded. The remaining proteins are candidates for further drug repositioning
analysis.
Rank
1
2
3
4
5
6
7
8
9
10
16
17
18
Protein
ALBU HUMAN
RARG1 HUMAN
DYR HUMAN
PTN1 HUMAN
RARA HUMAN
NOS3 HUMAN
HBB HUMAN
GSHR HUMAN
RXRA HUMAN
THB1 HUMAN
FA10 HUMAN
RARG2 HUMAN
RARB HUMAN
Docking score to Acitretin
-48
-46
-46
-45
-42
-42
-40
-39
-39
-39
-36
-36
-35
1OPL, shows that it is bound to a di erent inhibitor, and is in a conformation not ideal for binding
imatinib due to steric clashes. We then added mouse ABL PDB structures (with 98% sequence identity
to human ABL) into our pipeline, and they showed an ABL-imatinib interaction score of -58.4. This is
higher than the KIT-imatinib interaction in our current analysis and thus mouse-ABL would become
the top ranking target for imatinib instead of KIT. Imatinib is known to inhibit c-KIT, a protein
kinase linked to gastrointestinal stromal tumor, and was shown to be e ective for this cancer [12].
Thus, this KIT-imatinib interaction was correctly predicted in our docking analysis.
3 Discussion & Conclusion
Conceptually, inverse docking models a more realistic biological environment - once a drug enters the
body or speci c cells, which of the multitude of di erent proteins will it bind to? Inverse docking
methods have potential in many important areas of drug discovery, such as for predicting the unwanted side e ects for known and candidate drugs, determining druggable protein targets, and as we
particularly address in this study, predicting potential bene cial therapeutic uses for known drugs. To
our knowledge, this represents the rst time that inverse docking has been used for drug repositioning
analysis. Given the tremendous time and cost of drug discovery today, last estimated at 12 years
and $900 million US to discover and develop one new drug [14], inverse docking may allow for more
ecient drug discovery pipelines to be implemented. However, there are still many challenges to be
overcome for this type of analysis, which have been especially noted during our study.
Important implications arise from the limitations of current molecular docking methods. First,
docking is heavily dependent on the input protein structure. A strong point of this study was to
carefully lter for the quality of pockets prior to docking. For example, poorly resolved structures
cannot be reliably used in docking as the protein atom positions are already imprecise. Similarly,
pockets having nearby residues with low occupancy values or high temperature factor values are also
unreliable for docking. Pockets with nearby engineered mutations are not representative of wild-type
binding pockets, and pockets with gaps in their nearby observed sequence may be missing key residues.
Second, docking methods today do not easily handle protein exibility, presence of water and metal
ions, and accurate scoring. Protein exibility is partially compensated for when multiple structures
246
Li et al.
have been solved for the same protein in PDB. However, this a very small corner of protein conformational space, so it is expected that the predictive ability of inverse docking will be much improved with
the development of scalable exible-receptor exible-ligand docking methods. For protein-drug complexes with metals, our docking accurately predicted drug binding conformations but failed to predict
reasonable scores. We have tried to minimize scoring issues by only further analyzing proteins that
docked to known drugs with good scores, since these proteins are more likely to be in conformations
amenable for small molecule inhibition. These proteins are also more likely to be scored appropriately.
We are currently evaluating di erent scoring methods to better represent metal ions. In the future,
we plan to explore exible-protein exible-ligand docking with ICM and with other docking software.
One major challenge in inverse docking is comparing docking scores across di erent pockets, as
the score threshold should ideally be speci c to each receptor. In a best case scenario, a large set of
known inhibitors with known binding anities would be docked to each protein pocket, to determine
an appropriate docking score cut-o for expected small molecule binders. Such a task, however, would
require an immense amount of literature search, and is often impossible as many protein pockets have
not yet been characterized using diverse ligands. We have used a simple initial approximation by using
the docking scores of known protein-drug complexes from PDB and interactions from DrugBank as a
reference point for our receptor-speci c docking score cut-o s. In addition, we limit our investigation
of novel protein-drug interactions to only the dataset where known protein-drug interactions could
be reproduced. We are currently gathering more binding anity information from the literature to
better tailor the docking score cut-o s.
Finally, our study is limited by the number of known proteins and drugs in the input data set.
Having only 78 unique protein targets limits the utility of ProteinRank, as some of top-ranking targets
are likely to change when more proteins are added to the data set. By using only human protein
structures in our analysis, many informative structures were omitted - for example, the mouse ABL
structures. Thus, we are currently incorporating structures from other organisms aside from human,
when their sequence identity to the human protein is above 95%. In addition, we are including known
protein targets for experimental drugs as annotated in DrugBank - for example the LCK protein which
is a therapeutic target critical in T-cell receptor signaling [4] - but no drugs have yet been approved
for it.
Despite the limitations discussed, inverse docking opens a new avenue for computational drug discovery, with the potential to discover more about both adverse e ects and novel therapeutic targets
of existing drugs. Our analysis has begun to address some limitations by applying stringent pocket
quality lters, requiring targets to have a well-docked known drug before further analysis, and introducing receptor-speci c docking score cut-o s. By docking 1,055 known drugs to 1,548 pockets of 78
proteins we have found 52 interactions with potential pharmacological relevance, thus showing the
ability of the inverse docking method as a tool for drug repositioning. The analysis has also pointed
out many limitations of a large scale inverse docking analysis, which we are currently addressing, and
we anticipate that an improved pipeline will be able to better predict known and novel protein-drug
interactions. It is dicult to measure the accuracy of inverse docking, as previously unknown interactions may be false positives or novel predictions. However, the space of experimentally testing all
protein-drug combinations is vast, and large-scale inverse docking provides a computational lter to
select the most likely interactions to experimentally test.
References
[1] Abagyan, R., Totrov, M., and Kuznetsov, D., ICM: A new method for protein modeling and
design: Applications to docking and structure prediction from the distorted native conformation,
J. Comput. Chem., 15:488{506, 1994.
A Large-Scale Computational Approach to Drug Repositioning
247
[2] An, J., Totrov, M., and Abagyan, R., Pocketome via comprehensive identi cation and classi cation of ligand binding envelopes, Mol. Cell Proteomics, 4(6):752{761, 2005.
[3] Ashburn, T.T. and Thor, K.B., Drug repositioning: Identifying and developing new uses for
existing drugs, Nat. Rev. Drug Discov., 3(8):673{683, 2004.
[4] Bolen, J.B. and Brugge, J.S., Leukocyte protein tyrosine kinases: Potential targets for drug
discovery, Annu. Rev. Immunol, 15:371{404, 1997.
[5] Bourne, P.E., Addess, K.J., Bluhm, W.F., Chen, L., Deshpande, N., Feng, Z., Fleri, W., Green,
R., Merino-Ott, J.C., Townsend-Merino, W., Weissig, H., Westbrook, J., and Berman, H.M., The
distribution and query systems of the RCSB Protein Data Bank, Nucleic Acids Res., 32:D223{
D225, 2004.
[6] Bursulaya, B.D., Totrov, M., Abagyan, R., and Brooks, C.L. 3rd., Comparative study of several
algorithms for exible ligand docking, J. Comput. Aided Mol. Des., 17(11):755{763, 2003.
[7] Cavasotto, C.N., Ortiz, M.A., Abagyan, R.A., Piedra ta, F.J., In silico identi cation of novel
EGFR inhibitors with antiproliferative activity against cancer cells, Bioorg. Med. Chem. Lett.,
16(7):1969{1974, 2006.
[8] Chen, H., Lyne, P.D., Giordanetto, F., Lovell, T., and Li, J., On evaluating molecular-docking
methods for pose prediction and enrichment factors, J. Chem. Inf. Model., 46(1):401{415, 2006.
[9] Chen, Y.Z. and Zhi, D.G., Ligand-protein inverse docking and its potential use in the computer
search of protein targets of a small molecule, Proteins, 43(2):217{226, 2001.
[10] Chien, D.S., Sandri, R.B., and Tang-Liu, D.S., Systemic pharmacokinetics of acitretin, etretinate, isotretinoin, and acetylenic retinoids in guinea pigs and obese rats, Drug Metab. Dispos.,
20(2):211{217, 1992.
[11] Frantz, S., Drug discovery: Playing dirty, Nature, 437(7061):942{943, 2005.
[12] Fukunishi, Y., Mikami, Y., Kubota, S., and Nakamura, H., Multiple target screening method for
robust and accurate in silico ligand screening, J. Mol. Graph. Model., 25(1):61{70, 2006.
[13] Jorgensen, W.L., The many roles of computation in drug discovery, Science, 303(5665):1813{1818.
2004.
[14] Kola, I. and Landis, J., Can the pharmaceutical industry reduce attrition rates, Nat.
Discov., 3(8):711{715, 2004.
Rev. Drug
[15] Macchiarulo, A., Nobeli, I., and Thornton, J.M., Ligand selectivity and competition between
enzymes in silico, Nat. Biotechnol., 22(8):1039{1045, 2004.
[16] Perola, E., Walters, W.P., and Charifson, P.S., A detailed comparison of current docking and
scoring methods on systems of pharmaceutical relevance, Proteins, 56(2):235{249, 2004.
[17] Rockey, W.M. and Elcock, A.H., Progress toward virtual screening for drug side e ects, Proteins,
48(4):664{671, 2005.
[18] Wishart, D.S., Knox, C., Guo, A.C., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z., and
Woolsey, J., DrugBank: A comprehensive resource for in silico drug discovery and exploration,
Nucleic Acids Res., 34:D668{D672, 2006.