Diversity and determinants of the sigmoid septum and its impact on morphology of the outflow tract as revealed using cardiac computed tomography.

BACKGROUND: The sigmoid septum has been generally evaluated subjectively and qualitatively, without detailed examination of its diversity, impact on the morphology of the left ventricular outflow tract (LVOT), and anatomical background. METHODS: We enrolled 100 patients without any background cardiac diseases (67.5 ± 12.8 years old; 43% women) who underwent cardiac computed tomography. Basal septal morphology was evaluated using antero-superior and medial bulging angles (bidirectional angulation of the basal septum relative to the LVOT). The eccentricity index of the LVOT, area narrowing ratio (LVOT/virtual basal ring area), aortic-to-left ventricular axial angle (angulation of the aortic root relative to the left ventricle), and wedged height (non-coronary aortic sinus to inferior epicardium distance) were also quantified. RESULTS: The antero-superior bulging, medial bulging, aortic-to-left ventricular axial angles, LVOT eccentricity index, area narrowing ratio, and wedged height were 76° ± 17°, 166° ± 27°, 127° ± 9°, 1.8 ± 0.5, 1.0 ± 0.2, and 41.2 ± 9.1 mm, respectively. Both bulging angles were correlated with each other and contributed to the narrowing and deformation of the LVOT. Angulated aortic root was not correlated with either bidirectional septal bulge or LVOT narrowing. Clockwise rotation of the aortic root rotation was an independent predictor of prominent antero-superior septal bulge. Deeper aortic wedging was a common independent predictor of bidirectional septal bulge. CONCLUSIONS: The extent of septal bulge varies in normal hearts. Along with deep aortic wedging, the bidirectional bulge of the basal septum deforms and narrows the LVOT without affecting the virtual basal ring morphology.

Normative Aortic Valvar Measurements in Adults Using Cardiac Computed Tomography　- A Potential Guide to Further Sophisticate Aortic Valve-Sparing Surgery.

BACKGROUND: A thorough understanding of the anatomy of the aortic valve is necessary for aortic valve-sparing surgery. Normal valvar dimensions and their relationships in the living heart, however, have yet to be fully investigated in a 3-dimensional fashion.Methods and Results:In total, 123 consecutive patients (66±12 years, Men 63%) who underwent coronary computed tomographic angiography were enrolled. Mid-diastolic morphology of the aortic roots, including height of the interleaflet triangles, geometric height, free margin length of each leaflet, effective height, and coaptation length were measured using multiplanar reconstruction images. Average height of the interleaflet triangle, geometric height, free margin length, effective height, and the coaptation length were 17.3±1.8, 14.7±1.3, 32.6±3.6, 8.6±1.4, and 3.2±0.8 mm, respectively. The right coronary aortic leaflet displayed the longest free margin length and shortest geometric height. Geometric height, free margin length, and effective height showed positive correlations with aortic root dimensions. Coaptation length, however, remained constant regardless of aortic root dimensions. CONCLUSIONS: Diversities, as well as characteristic relationships among each value involving the aortic root, were identified using living-heart datasets. The aortic leaflets demonstrated compensatory elongation along with aortic root dilatation to maintain constant coaptation length. These measurements will serve as the standard value for revealing the underlying mechanism of aortic regurgitation to plan optimal aortic valve-sparing surgery.

Three-dimensional volumetric measurement of the aortic root compared to standard two-dimensional measurements using cardiac computed tomography.

INTRODUCTION: Two-dimensional measurements are self-evidently limited when seeking accurately to represent the three-dimensional complexity of the aortic root. Volumetric measurement, therefore, seems an ideal alternative for a more accurate assessment. MATERIALS AND METHODS: We retrospectively analyzed 123 individuals undergoing cardiac computed tomography. We measured the dimensions of the sinuses of Valsalva using routine multiplanar short axis imaging. Three conventional two-dimensional methods were applied to measure the dimensions of the sinuses. These involved bisecting center of sinus-to-center of interleaflet triangle measures, along with center of sinus-to-center of sinus, and largest sinus-to-sinus measurements. We then quantified the volumes of the root using the volume-rendering method. RESULTS: The mean dimensions of the sinuses were significantly greater when measured using the largest sinus-to-sinus method as opposed to center of sinus-to-center of interleaflet triangle and center of sinus-to-center of sinus methods (33.6 ± 3.6 mm vs. 31.1 ± 3.1 mm and 30.9 ± 3.3 mm, p < .0001). The mean root volume of 13.6 ± 4.2 ml showed the strongest correlation with the mean dimensions of the sinuses of Valsalva measured using the bisecting method (R2 = .8401, p < .0001). CONCLUSIONS: By using two- and three-dimensional measurements, we have provided average data for the structurally normal aortic root. The differences and correlations encountered should be noted when evaluating and following changes in the diseased root.

Update of the GRIP web service.

G protein-coupled receptors (GPCRs) can form homodimers, heterodimers, or higher-order molecular complexes (oligomers). The reports on the change of functions through the oligomerization have been accumulated. Inhibition of GPCR oligomerization without affecting the protomer's overall structure would clarify the oligomer-specific functions although inhibition experiments are costly and require accurate information about the interface location. Unfortunately, the number of experimentally determined interfaces is limited. The precise prediction of the oligomerization interfaces is, therefore, useful for inhibition experiments to examine the oligomer-specific functions, which would accelerate investigations of the GPCR signaling. However, interface prediction for GPCR oligomerization is difficult because different GPCR subtypes belonging to the same subfamily often use different structural regions as their interfaces. We previously developed a high-performance method to predict the interfaces for GPCR oligomerization, by identifying the conserved surfaces with the sequence and structure information. Then, the structural characteristic of a GPCR structure is regarded to be a thick-tube like conformation that is approximately perpendicular to the membrane plane. Our method had successfully predicted all of the interfaces available on that day. We had launched a web server for our interface prediction of GPCRs (GRIP). We have improved the previous version of GRIP server and enhanced its usability. First, we discarded the approximation of the GPCR structure as the thick-tube-like conformation. This improvement increased the number of structures for the prediction. Second, the FUGUE-based template recommendation service was introduced to facilitate the choice of an appropriate structure for the prediction. The new prediction server is available at http://grip.b.dendai.ac.jp/∼grip/.

Ascending aortic elongation and correlative change in overall configuration of the proximal aorta in elderly patients with severe aortic stenosis.

BACKGROUND: Configurational changes in the proximal aorta are relevant to the procedural difficulty of transcatheter aortic valve implantation (TAVI). Among several morphological changes involving the ascending aorta, elongation is characteristics of elderly patients with aortic stenosis and can compromise the success and safety of TAVI. However, the effect of ascending aortic elongation on the overall morphology of the proximal aorta has not been established. AIMS: Our primary purpose was to investigate the effect of ascending aortic elongation on structural changes in the proximal aorta in TAVI candidates. MATERIALS & METHODS: In total, 121 consecutive patients with severe aortic stenosis (mean age, 84.5 ± 5.3 years; 69% women) who had undergone preprocedural computed tomography before TAVI were enrolled. We examined the structural anatomy of the proximal aorta in detail, focusing on its elongation, dilatation, tilting, rotation, and wedging. RESULTS: The mean length of the ascending aorta was 68.0 ± 9.2 mm, and the length was significantly correlated with dilatation (R = .278, p = .002), rightward tilting (R = .437, p < .001), clockwise rotation (R = .228, p = .018), and deep wedging (R = -.366, p < .001) of the proximal aorta. Elongation of the ascending aorta was correlated with dilatation, rightward tilting, clockwise rotation, and deep wedging of the proximal aorta in an elderly population with severe aortic stenosis. DISCUSSION: Appreciation of the clinical anatomy around the proximal aorta is required for clinicians involved in TAVI to estimate the procedural difficulty. CONCLUSION: Elongation of the ascending aorta was associated with dilatation, rightward tilting, clockwise rotation, and deep wedging of the proximal aorta.

Localized basal left ventricular dyssynchrony induced by manifest accessory pathway: Successful differentiation from cardiac involvement of sarcoidosis with administration of flecainide acetate.

We present a patient with non-cardiac sarcoidosis complicated with manifest ventricular preexcitation. Initially, cardiac involvement of sarcoidosis was suspected from the echocardiographic findings showing localized hypokinesia at the left ventricular basal inferior wall. We, however, considered that the hypokinesia was a preexcitation-induced mechanical dyssynchrony rather than cardiac sarcoidosis, because polarities of the delta-waves indicated a left ventricular inferior accessory pathway. Temporal administration of oral flecainide acetate eliminated the basal left ventricular motion abnormality. Accordingly, we could successfully differentiate the mechanism of hypokinesia. In this context, we could rule out cardiac sarcoidosis, and initiation of glucocorticoid therapy was reasonably withheld.

The rotational position of the aortic root related to its underlying ventricular support.

We aimed to assess the relationship of the rotational position of the aortic root to its underlying ventricular support, and to the position of the inferior margin of the membranous septum, which serves as a surrogate of the atrioventricular conduction axis. We analyzed 40 normal heart specimens (19 children, 21 adults). The inferior margin of the membranous septum was measured relative to the virtual basal ring. The rotational position of the aortic root was determined by assessing the relationship of the aortic leaflet of the mitral valve to the interleaflet triangle between the non- and left coronary leaflets. The extent of supporting fibrous versus myocardial tissues was measured. We also performed a similar investigation of 30 adult computed tomographic data sets. The median age was 0.25 years (44% male) for children, and 64 years (33% male) for adults. The aortic root was positioned centrally in 22 specimens (55%), rotated counterclockwise in 6 (15%), and clockwise in 12 (30%). In the setting of counterclockwise rotation, 53.4% (median) of the supporting circumference was myocardial, as opposed to 41.4% (median) in those with centrally positioned roots, and 31.9% (median) in those with clockwise rotation (P < 0.0001). The position of the inferior margin of the membranous septum was not associated with the rotational position. Analysis of the 30 adult computed tomographic data sets (median age 66.5 years, 57% male) confirmed the positive relationship between clockwise rotation of the aortic root and an increase in the extent of fibrous as opposed to myocardial support. The rotational position of the aortic root correlates with variation in the extent of its fibrous as opposed to myocardial ventricular support, but not with the position of the inferior margin of the membranous septum relative to the virtual basal ring. Clin. Anat. 32:1107-1117, 2019. © 2019 Wiley Periodicals, Inc.

Distorted antibody repertoire developed in the absence of pre-B cell receptor formation.

The pre-B cell receptor (pre-BCR), consisting of the µ heavy chain (µHC) and the surrogate light chain (SLC, Vpre-B and λ5), plays important roles during B cell development. The formation of the pre-BCR, which enables the nascent immunoglobulin HC to associate with the SLC, is considered a prerequisite for B cell development. However, a significant number of peripheral mature (leaky) B cells exist in SLC-deficient mice. These leaky B cells develop in the absence of pre-BCR and do not undergo the pre-BCR checkpoint. The antibody repertoires of leaky B cells thus reflect the absence of pre-BCR function. To investigate how the absence of the pre-BCR is circumvented by these leaky-B cells and examine the effect of the pre-BCR checkpoint on the antibody system, we analyzed the antibody repertoires of λ5-deficient (λ5-/-) mice using next-generation sequencing. In λ5-/- mice, spleen B cells displayed different patterns of VDJ-usage, relative to those in wild-type (WT) mice. Moreover, leaky B cells were neither derived from unusual B2 cells, characterized by particular LC gene rearrangements in the absence of pre-BCR signaling, nor from B1 cells, originating from different B cell progenitors. Analysis of the CDR-H3 amino acid sequences of µ-chain repertoires revealed that certain bone marrow B cells with particular CDR-H3 profiles undergo clonal expansion in λ5-/- mice. Part of these CDR-H3s contain arginine(s) in the middle of the CDR-H3 loop in λ5-/- mice, whereas few arginine(s) exist in this middle loop in WT CDR-H3s in the absence of clonal expansion. This CDR-H3 feature in λ5-/- mice presumably reflects the role of the pre-BCR in autoantibody regulation, since arginine(s) are often found in the antigen-binding site of autoantibodies. Here, we present a unique viewpoint on the role of pre-BCR, by assessing the whole antibody repertoire formed in SLC-deficient mice.

Optimal reconstruction of left ventricular outflow tract obstruction before surgical myectomy in a case with hypertrophic obstructive cardiomyopathy.

We present optimally reconstructed three-dimensional computed tomography images of left ventricular outflow obstruction, comprehensive left ventriculography, and comparable intraoperative transesophageal echocardiography, as well as serial operative pictures, to facilitate the understanding of live-heart anatomy of hypertrophic obstructive cardiomyopathy. As shown in this case, detailed morphological analysis around the left ventricular outflow tract using preoperative computed tomography would be feasible and useful. The present case highlights the importance of obtaining complete three-dimensional information present in the acquired computed tomography dataset because computed tomography is not entirely noninvasive or free of radiation exposure and contrast material.

Serial observation of electrocardiographic responses to corticosteroid therapy in a patient with right ventricular-predominant cardiac sarcoidosis.

Predominant or isolated right ventricular involvement in cardiac sarcoidosis is uncommon, but should always be considered in a case of right ventricular hypertrophy combined with ventricular arrhythmia and/or conduction disturbance. Although improvement in right ventricular hypertrophy and atrioventricular conduction disturbance following corticosteroid therapy has been reported, the detailed serial electrocardiographic responses during corticosteroid therapy, as well as temporal changes in the electrocardiographic, biochemical, and morphological responses, have not been reported. We describe the clinical course and supportive imaging findings of reversible right ventricular hypertrophy and cardiac conduction disturbance in a case of right ventricular-predominant cardiac sarcoidosis.

Deciphering antigen-responding antibody repertoires by using next-generation sequencing and confirming them through antibody-gene synthesis.

Vast diversity and high specificity of antigen recognition by antibodies are hallmarks of the acquired immune system. Although the molecular mechanisms that yield the extremely large antibody repertoires are precisely understood, comprehensive description of the global antibody repertoire generated in individual bodies has been hindered by the lack of powerful measures. To obtain holistic understanding of the antibody-repertoire space, we used next-generation sequencing (NGS) to analyze the deep profiles of naive and antigen-responding repertoires of the IgM, IgG1, and IgG2c classes formed in individual mice. The overall landscapes of naive IgM repertoires were almost the same for each mouse, whereas those of IgG1 and IgG2c differed considerably among naive individuals. Next, we immunized mice with a model antigen, nitrophenol (NP)-hapten linked to chicken γ-globulin (CGG) carrier, and compared the antigen-responding repertoires in individual mice. To extract the complete antigen response, we developed an intelligible method for detecting common components of antigen-responding repertoires. The major responding antibodies were IGHV1-72/IGHD1-1/IGHJ2 for NP-hapten and IGHV9-3/IGHD3-1/IGHJ2 for CGG-carrier protein. The antigen-binding specificities of the identified antibodies were confirmed through ELISA after antibody-gene synthesis and expression of the corresponding NGS reads. Thus, we deciphered antigen-responding antibody repertoires by inclusively analyzing the antibody-repertoire space generated in individual bodies by using NGS, which avoided inadvertent omission of key antibody repertoires.

GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-dimers or higher-order molecular complexes. Many GPCRs exert a wide variety of molecular functions by forming specific combinations of GPCR subtypes. In addition, some GPCRs are reportedly associated with diseases. GPCR oligomerization is now recognized as an important event in various biological phenomena, and many researchers are investigating this subject. We have developed a support vector machine (SVM)-based method to predict interacting pairs for GPCR oligomerization, by integrating the structure and sequence information of GPCRs. The performance of our method was evaluated by the Receiver Operating Characteristic (ROC) curve. The corresponding area under the curve was 0.938. As far as we know, this is the only prediction method for interacting pairs among GPCRs. Our method could accelerate the analyses of these interactions, and contribute to the elucidation of the global structures of the GPCR networks in membranes. Proteins 2016; 84:1224-1233. © 2016 Wiley Periodicals, Inc.

Identification of novel target genes specifically activated by deregulated E2F in human normal fibroblasts.

The transcription factor E2F is the principal target of the tumor suppressor pRB. E2F plays crucial roles not only in cell proliferation by activating growth-related genes but also in tumor suppression by activating pro-apoptotic and growth-suppressive genes. We previously reported that, in human normal fibroblasts, the tumor suppressor genes ARF, p27(Kip1) and TAp73 are activated by deregulated E2F activity induced by forced inactivation of pRB, but not by physiological E2F activity induced by growth stimulation. In contrast, growth-related E2F targets are activated by both E2F activities, underscoring the roles of deregulated E2F in tumor suppression in the context of dysfunctional pRB. In this study, to further understand the roles of deregulated E2F, we explored new targets that are specifically activated by deregulated E2F using DNA microarray. The analysis identified nine novel targets (BIM, RASSF1, PPP1R13B, JMY, MOAP1, RBM38, ABTB1, RBBP4 and RBBP7), many of which are involved in the p53 and RB tumor suppressor pathways. Among these genes, the BIM gene was shown to be activated via atypical E2F-responsive promoter elements and to contribute to E2F1-mediated apoptosis. Our results underscore crucial roles of deregulated E2F in growth suppression to counteract loss of pRB function.

Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3).

Dengue viruses (DEN) are classified into four serotypes (DEN1-DEN4) exhibiting high sequence and structural similarities, and infections by multiple serotypes can lead to the deadly dengue hemorrhagic fever. Here, we aim at characterizing the thermodynamic stability of DEN envelope protein domain III (ED3) during its evolution, and we report a structural analysis of DEN4wt ED3 combined with a systematic mutational analysis of residues 310 and 387. Molecular modeling based on our DEN3 and DEN4 ED3 structures indicated that the side-chains of residues 310/387, which are Val(310)/Ile(387) and Met(310)/Leu(387) in DEN3wt and DEN4wt, respectively, could be structurally compensated, and that a "size switch type repacking" might have occurred at these sites during the evolution of DEN into its four serotypes. This was experimentally confirmed by a 10°C and 5°C decrease in the thermal stability of, respectively, DEN3 ED3 variants with Met(310)/Ile(387) and Val(310)/Leu(387), whereas the variant with Met(310)/Leu(387), which contains a double mutation, had the same stability as the wild type DEN3. Namely, the Met310Val mutation should have preceded the Leu387Ile mutation in order to maintain the tight internal packing of ED3 and thus its thermodynamic stability. This view was confirmed by a phylogenetic reconstruction indicating that a common DEN ancestor would have Met(310)/Leu(387), and the intermediate node protein, Val(310)/Leu(387), which then mutated to the Val(310)/Ile(387) pair found in the present DEN3. The hypothesis was further confirmed by the observation that all of the present DEN viruses exhibit only stabilizing amino acid pairs at the 310/387 sites.

VCIP135 deubiquitinase and its binding protein, WAC, in p97ATPase-mediated membrane fusion.

Two distinct p97 membrane fusion pathways are required for Golgi biogenesis: the p97/p47 and p97/p37 pathways. VCIP135 is necessary for both pathways, while its deubiquitinating activity is required only for the p97/p47 pathway. We have now identified a novel VCIP135-binding protein, WAC. WAC localizes to the Golgi as well as the nucleus. In Golgi membranes, WAC is involved in a complex containing VCIP135 and p97. WAC directly binds to VCIP135 and increases its deubiquitinating activity. siRNA experiments revealed that WAC is required for Golgi biogenesis. In an in vitro Golgi reformation assay, WAC was necessary only for p97/p47-mediated Golgi reassembly, but not for p97/p37-mediated reassembly. WAC is hence thought to function in p97/p47-mediated Golgi membrane fusion by activating the deubiquitinating function of VCIP135. We also showed that the two p97 pathways function in ER membrane fusion as well. An in vitro ER reformation assay revealed that both pathways required VCIP135 but not its deubiquitinating activity for their ER membrane fusion. This was consistent with the finding that WAC is unnecessary for p97-mediated ER membrane fusion.

The rs6983267 SNP is associated with MYC transcription efficiency, which promotes progression and worsens prognosis of colorectal cancer.

BACKGROUND: The oncogenic single nucleotide polymorphism rs6983267, located on 8q24.21, may affect copy number aberrations and/or expression profiles in colorectal cancer (CRC). We investigated the role of this single nucleotide polymorphism in the clinical outcome of CRC. METHODS: Array comparative genomic hybridization (aCGH) and oligomicroarrays were performed on cancer cells from 157 primary CRC tissues. Expression profiles were analyzed by means of extraction expression module (EEM) analyses. Mutations in TP53, KRAS, and BRAF and microsatellite instability were also examined in 107 of the 157 cases. RESULTS: aCGH analysis revealed two clusters; more frequent genomic copy number alteration (CNA) was observed in the 89 cases in cluster B than in the 18 cases in cluster A. The average CNA was higher in samples containing the major allele (GT/TT) of rs6983267 than in those containing the minor allele (GG). Additionally, MYC expression was the highest in samples containing the GG allele (n = 18), followed by the GT and TT alleles (n = 41 and 48, respectively). EEM analysis revealed dominant up-regulation of MYC in samples containing the minor allele. Moreover, the presence of the minor allele in a MYC-positive, CNA-negative context predicted a poorer prognosis than the presence of the major allele in a MYC-negative, CNA-positive context in CRC. CONCLUSIONS: The presence of the minor allele of rs6983267 at 8q24.21 worsened the prognosis of CRC through up-regulation of MYC transcription. Furthermore, progression of CRC may require global CNA in the presence of the major allele and with lack of MYC transcription.

Notch-Hes1 pathway is required for the development of IL-17-producing γδ T cells.

Unlike conventional T cells, which are exported from the thymus as naive cells and acquire effector functions upon antigen encounter in the periphery, a subset of γδ T cells differentiates into effectors that produce IL-17 within the fetal thymus. We demonstrate here that intrathymic development of the naturally occurring IL-17-producing γδ T cells is independent of STAT3 and partly dependent on RORγt. Comparative gene-expression analysis identified Hes1, one of the basic helix-loop-helix proteins involved in Notch signaling, as a factor specifically expressed in IL-17-producing γδ T cells. Hes1 is critically involved in the development of IL-17-producing γδ T cells, as evidenced by their severe decrease in the thymi of Hes1-deficient fetal mice. Delta-like 4 (Dll4)-expressing stromal cells support the development of IL-17-producing γδ T cells in vitro. In addition, conditional Hes1 ablation in peripheral γδ T cells decreases their IL-17 production but not their IFN-γ production. These results reveal a unique differentiation pathway of IL-17-producing γδ T cells.

Functional region prediction with a set of appropriate homologous sequences--an index for sequence selection by integrating structure and sequence information with spatial statistics.

BACKGROUND: The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions. Various methods, such as Evolutionary Trace, have been developed based on this strategy. In such approaches, the conserved residues are identified through comparisons of homologous amino acid sequences. Therefore, the selection of homologous sequences is a critical step. It is empirically known that a certain degree of sequence divergence in the set of homologous sequences is required for the identification of conserved residues. However, the development of a method to select homologous sequences appropriate for the identification of conserved residues has not been sufficiently addressed. An objective and general method to select appropriate homologous sequences is desired for the efficient prediction of functional regions. RESULTS: We have developed a novel index to select the sequences appropriate for the identification of conserved residues, and implemented the index within our method to predict the functional regions of a protein. The implementation of the index improved the performance of the functional region prediction. The index represents the degree of conserved residue clustering on the tertiary structure of the protein. For this purpose, the structure and sequence information were integrated within the index by the application of spatial statistics. Spatial statistics is a field of statistics in which not only the attributes but also the geometrical coordinates of the data are considered simultaneously. Higher degrees of clustering generate larger index scores. We adopted the set of homologous sequences with the highest index score, under the assumption that the best prediction accuracy is obtained when the degree of clustering is the maximum. The set of sequences selected by the index led to higher functional region prediction performance than the sets of sequences selected by other sequence-based methods. CONCLUSIONS: Appropriate homologous sequences are selected automatically and objectively by the index. Such sequence selection improved the performance of functional region prediction. As far as we know, this is the first approach in which spatial statistics have been applied to protein analyses. Such integration of structure and sequence information would be useful for other bioinformatics problems.

DROP: an SVM domain linker predictor trained with optimal features selected by random forest.

MOTIVATION: Biologically important proteins are often large, multidomain proteins, which are difficult to characterize by high-throughput experimental methods. Efficient domain/boundary predictions are thus increasingly required in diverse area of proteomics research for computationally dissecting proteins into readily analyzable domains. RESULTS: We constructed a support vector machine (SVM)-based domain linker predictor, DROP (Domain linker pRediction using OPtimal features), which was trained with 25 optimal features. The optimal combination of features was identified from a set of 3000 features using a random forest algorithm complemented with a stepwise feature selection. DROP demonstrated a prediction sensitivity and precision of 41.3 and 49.4%, respectively. These values were over 19.9% higher than those of control SVM predictors trained with non-optimized features, strongly suggesting the efficiency of our feature selection method. In addition, the mean NDO-Score of DROP for predicting novel domains in seven CASP8 FM multidomain proteins was 0.760, which was higher than any of the 12 published CASP8 DP servers. Overall, these results indicate that the SVM prediction of domain linkers can be improved by identifying optimal features that best distinguish linker from non-linker regions.