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1.  Hydrogen Peroxide Induce Human Cytomegalovirus Replication through the Activation of p38-MAPK Signaling Pathway 
Viruses  2015;7(6):2816-2833.
Human cytomegalovirus (HCMV) is a major risk factor in transplantation and AIDS patients, which induces high morbidity and mortality. These patients infected with HCMV experience an imbalance of redox homeostasis that cause accumulation of reactive oxygen species (ROS) at the cellular level. H2O2, the most common reactive oxygen species, is the main byproduct of oxidative metabolism. However, the function of H2O2 on HCMV infection is not yet fully understood and the effect and mechanism of N-acetylcysteine (NAC) on H2O2-stimulated HCMV replication is unclear. We, therefore, examined the effect of NAC on H2O2-induced HCMV production in human foreskin fibroblast cells. In the present study, we found that H2O2 enhanced HCMV lytic replication through promoting major immediate early (MIE) promoter activity and immediate early (IE) gene transcription. Conversely, NAC inhibited H2O2-upregulated viral IE gene expression and viral replication. The suppressive effect of NAC on CMV in an acute CMV-infected mouse model also showed a relationship between antioxidants and viral lytic replication. Intriguingly, the enhancement of HCMV replication via supplementation with H2O2 was accompanied with the activation of the p38 mitogen-activated protein kinase pathway. Similar to NAC, the p38 inhibitor SB203580 inhibited H2O2-induced p38 phosphorylation and HCMV upregulation, while upregulation of inducible ROS was unaffected. These results directly relate HCMV replication to H2O2, suggesting that treatment with antioxidants may be an attractive preventive and therapeutic strategy for HCMV.
doi:10.3390/v7062748
PMCID: PMC4488715  PMID: 26053925
CMV; H2O2; IE1; viral replication; antioxidants; p38-MAPK
2.  Finding Alternative Expression Quantitative Trait Loci by Exploring Sparse Model Space 
Journal of Computational Biology  2014;21(5):385-393.
Abstract
Sparse modeling, a feature selection method widely used in the machine-learning community, has been recently applied to identify associations in genetic studies including expression quantitative trait locus (eQTL) mapping. These genetic studies usually involve high dimensional data where the number of features is much larger than the number of samples. The high dimensionality of genetic data introduces a problem that there exist multiple solutions for optimizing a sparse model. In such situations, a single optimization result provides only an incomplete view of the data and lacks power to find alternative features associated with the same trait. In this article, we propose a novel method aimed to detecting alternative eQTLs where two genetic variants have alternative relationships regarding their associations with the expression of a particular gene. Our method accomplishes this goal by exploring multiple solutions sampled from the solution space. We proved our method theoretically and demonstrated its usage on simulated data. We then applied our method to a real eQTL data and identified a set of alternative eQTLs with potential biological insights. Additionally, these alternative eQTLs implicate a network view of understanding gene regulation.
doi:10.1089/cmb.2014.0026
PMCID: PMC4010169  PMID: 24689773
expression quantitative trait locus (eQTL) mapping; redundancy; sparse modeling
3.  Inferential modeling of 3D chromatin structure 
Nucleic Acids Research  2015;43(8):e54.
For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen.
doi:10.1093/nar/gkv100
PMCID: PMC4417147  PMID: 25690896
4.  An Integrative Computational Approach for Prioritization of Genomic Variants 
PLoS ONE  2014;9(12):e114903.
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.
doi:10.1371/journal.pone.0114903
PMCID: PMC4266634  PMID: 25506935
5.  HubAlign: an accurate and efficient method for global alignment of protein–protein interaction networks 
Bioinformatics  2014;30(17):i438-i444.
Motivation: High-throughput experimental techniques have produced a large amount of protein–protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency.
Results: This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins.
Availability: HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip
Contact: jinboxu@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btu450
PMCID: PMC4147903  PMID: 25161231
6.  MRFalign: Protein Homology Detection through Alignment of Markov Random Fields 
PLoS Computational Biology  2014;10(3):e1003500.
Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.
Author Summary
Sequence-based protein homology detection has been extensively studied, but it remains very challenging for remote homologs with divergent sequences. So far the most sensitive methods employ HMM-HMM comparison, which models a protein family using HMM (Hidden Markov Model) and then detects homologs using HMM-HMM alignment. HMM cannot model long-range residue interaction patterns and thus, carries very little information regarding the global 3D structure of a protein family. As such, HMM comparison is not sensitive enough for distantly-related homologs. In this paper, we present an MRF-MRF comparison method for homology detection. In particular, we model a protein family using Markov Random Fields (MRF) and then detect homologs by MRF-MRF alignment. Compared to HMM, MRFs are able to model long-range residue interaction pattern and thus, contains information for the overall 3D structure of a protein family. Consequently, MRF-MRF comparison is much more sensitive than HMM-HMM comparison. To implement MRF-MRF comparison, we have developed a new scoring function to measure the similarity of two MRFs and also an efficient ADMM algorithm to optimize the scoring function. Experiments confirm that MRF-MRF comparison indeed outperforms HMM-HMM comparison in terms of both alignment accuracy and remote homology detection, especially for mainly beta proteins.
doi:10.1371/journal.pcbi.1003500
PMCID: PMC3967925  PMID: 24675572
7.  Lynx: a database and knowledge extraction engine for integrative medicine 
Nucleic Acids Research  2013;42(Database issue):D1007-D1012.
We have developed Lynx (http://lynx.ci.uchicago.edu)—a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from >35 public databases and private collections, as well as manually curated data from our group and collaborators. Lynx provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization to assist the user in extracting meaningful knowledge from LynxKB and experimental data, whereas its service-oriented architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces.
doi:10.1093/nar/gkt1166
PMCID: PMC3965040  PMID: 24270788
8.  Protein threading using context-specific alignment potential 
Bioinformatics  2013;29(13):i257-i265.
Motivation: Template-based modeling, including homology modeling and protein threading, is the most reliable method for protein 3D structure prediction. However, alignment errors and template selection are still the main bottleneck for current template-base modeling methods, especially when proteins under consideration are distantly related.
Results: We present a novel context-specific alignment potential for protein threading, including alignment and template selection. Our alignment potential measures the log-odds ratio of one alignment being generated from two related proteins to being generated from two unrelated proteins, by integrating both local and global context-specific information. The local alignment potential quantifies how well one sequence residue can be aligned to one template residue based on context-specific information of the residues. The global alignment potential quantifies how well two sequence residues can be placed into two template positions at a given distance, again based on context-specific information. By accounting for correlation among a variety of protein features and making use of context-specific information, our alignment potential is much more sensitive than the widely used context-independent or profile-based scoring function. Experimental results confirm that our method generates significantly better alignments and threading results than the best profile-based methods on several large benchmarks. Our method works particularly well for distantly related proteins or proteins with sparse sequence profiles because of the effective integration of context-specific, structure and global information.
Availability: http://raptorx.uchicago.edu/download/.
Contact: jinboxu@gmail.com
doi:10.1093/bioinformatics/btt210
PMCID: PMC3694651  PMID: 23812991
9.  Predicting protein contact map using evolutionary and physical constraints by integer programming 
Bioinformatics  2013;29(13):i266-i273.
Motivation: Protein contact map describes the pairwise spatial and functional relationship of residues in a protein and contains key information for protein 3D structure prediction. Although studied extensively, it remains challenging to predict contact map using only sequence information. Most existing methods predict the contact map matrix element-by-element, ignoring correlation among contacts and physical feasibility of the whole-contact map. A couple of recent methods predict contact map by using mutual information, taking into consideration contact correlation and enforcing a sparsity restraint, but these methods demand for a very large number of sequence homologs for the protein under consideration and the resultant contact map may be still physically infeasible.
Results: This article presents a novel method PhyCMAP for contact map prediction, integrating both evolutionary and physical restraints by machine learning and integer linear programming. The evolutionary restraints are much more informative than mutual information, and the physical restraints specify more concrete relationship among contacts than the sparsity restraint. As such, our method greatly reduces the solution space of the contact map matrix and, thus, significantly improves prediction accuracy. Experimental results confirm that PhyCMAP outperforms currently popular methods no matter how many sequence homologs are available for the protein under consideration.
Availability: http://raptorx.uchicago.edu.
Contact: jinboxu@gmail.com
doi:10.1093/bioinformatics/btt211
PMCID: PMC3694661  PMID: 23812992
10.  A position-specific distance-dependent statistical potential for protein structure and functional study 
Structure(London, England:1993)  2012;20(6):1118-1126.
Summary
Although studied extensively, designing highly accurate protein energy potential is still challenging. A lot of knowledge-based statistical potentials are derived from the inverse of the Boltzmann law and consist of two major components: observed atomic interacting probability and reference state. These potentials mainly distinguish themselves in the reference state and use a similar simple counting method to estimate the observed probability, which is usually assumed to correlate with only atom types. This paper takes a rather different view on the observed probability and parameterizes it by the protein sequence profile context of the atoms and the radius of the gyration, in addition to atom types. Experiments confirm that our position-specific statistical potential outperforms currently the popular ones in several decoy discrimination tests. Our results imply that in addition to reference state, the observed probability also makes energy potentials different and evolutionary information greatly boost performance of energy potentials.
doi:10.1016/j.str.2012.04.003
PMCID: PMC3372698  PMID: 22608968
11.  Protein structure alignment beyond spatial proximity 
Scientific Reports  2013;3:1448.
Protein structure alignment is a fundamental problem in computational structure biology. Many programs have been developed for automatic protein structure alignment, but most of them align two protein structures purely based upon geometric similarity without considering evolutionary and functional relationship. As such, these programs may generate structure alignments which are not very biologically meaningful from the evolutionary perspective. This paper presents a novel method DeepAlign for automatic pairwise protein structure alignment. DeepAlign aligns two protein structures using not only spatial proximity of equivalent residues (after rigid-body superposition), but also evolutionary relationship and hydrogen-bonding similarity. Experimental results show that DeepAlign can generate structure alignments much more consistent with manually-curated alignments than other automatic tools especially when proteins under consideration are remote homologs. These results imply that in addition to geometric similarity, evolutionary information and hydrogen-bonding similarity are essential to aligning two protein structures.
doi:10.1038/srep01448
PMCID: PMC3596798  PMID: 23486213
12.  A Probabilistic Graphical Model for Ab Initio Folding 
Despite significant progress in recent years, ab initio folding is still one of the most challenging problems in structural biology. This paper presents a probabilistic graphical model for ab initio folding, which employs Conditional Random Fields (CRFs) and directional statistics to model the relationship between the primary sequence of a protein and its three-dimensional structure. Different from the widely-used fragment assembly method and the lattice model for protein folding, our graphical model can explore protein conformations in a continuous space according to their probability. The probability of a protein conformation reflects its stability and is estimated from PSI-BLAST sequence profile and predicted secondary structure. Experimental results indicate that this new method compares favorably with the fragment assembly method and the lattice model.
doi:10.1007/978-3-642-02008-7_5
PMCID: PMC3583211  PMID: 23459639
protein structure prediction; ab initio folding; conditional random fields (CRFs); directional statistics; fragment assembly; lattice model
13.  RaptorX: exploiting structure information for protein alignment by statistical inference 
Proteins  2011;79(Suppl 10):161-171.
This paper presents RaptorX, a statistical method for template-based protein modeling that improves alignment accuracy by exploiting structural information in a single or multiple templates. RaptorX consists of three major components: single-template threading, alignment quality prediction and multiple-template threading. This paper summarizes the methods employed by RaptorX and presents its CASP9 result analysis, aiming to identify major bottlenecks with RaptorX and template-based modeling and hopefully directions for further study. Our results show that template structural information helps a lot with both single-template and multiple-template protein threading especially when closely-related templates are unavailable and there is still large room for improvement in both alignment and template selection. The RaptorX web server is available at http://raptorx.uchicago.edu.
doi:10.1002/prot.23175
PMCID: PMC3226909  PMID: 21987485
single-template threading; multiple-template threading; alignment quality prediction; probabilistic alignment; multiple protein alignment; CASP
14.  Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling 
Bioinformatics  2011;27(18):2537-2545.
Motivation: Building an accurate alignment of a large set of distantly related protein structures is still very challenging.
Results: This article presents a novel method 3DCOMB that can generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise alignments. 3DCOMB is unique in that it makes use of both local and global structure environments, combined by a statistical learning method, to accurately identify highly similar fragment blocks (HSFBs) among all proteins to be aligned. By extending the alignments of these HSFBs, 3DCOMB can quickly generate an accurate MSA without using progressive alignment. 3DCOMB significantly excels others in aligning distantly related proteins. 3DCOMB can also generate correct alignments for functionally similar regions among proteins of very different structures while many other MSA tools fail. 3DCOMB is useful for many real-world applications. In particular, it enables us to find out that there is still large improvement room for multiple template homology modeling while several other MSA tools fail to do so.
Availability: 3DCOMB is available at http://ttic.uchicago.edu/~jinbo/software.htm.
Contact: jinboxu@gmail.com
Supplementary Information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btr432
PMCID: PMC3167051  PMID: 21791532
15.  A computational framework for boosting confidence in high-throughput protein-protein interaction datasets 
Genome Biology  2012;13(8):R76.
Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-positive and false-negative rates. Coev2Net is easily applied to thousands of binary protein interactions and has superior predictive performance over existing methods. We experimentally validate selected high-confidence predictions in the human MAPK network and show that predicted interfaces are enriched for cancer -related or damaging SNPs. Coev2Net can be downloaded at http://struct2net.csail.mit.edu.
doi:10.1186/gb-2012-13-8-r76
PMCID: PMC4053744  PMID: 22937800
16.  A conditional neural fields model for protein threading 
Bioinformatics  2012;28(12):i59-i66.
Motivation: Alignment errors are still the main bottleneck for current template-based protein modeling (TM) methods, including protein threading and homology modeling, especially when the sequence identity between two proteins under consideration is low (<30%).
Results: We present a novel protein threading method, CNFpred, which achieves much more accurate sequence–template alignment by employing a probabilistic graphical model called a Conditional Neural Field (CNF), which aligns one protein sequence to its remote template using a non-linear scoring function. This scoring function accounts for correlation among a variety of protein sequence and structure features, makes use of information in the neighborhood of two residues to be aligned, and is thus much more sensitive than the widely used linear or profile-based scoring function. To train this CNF threading model, we employ a novel quality-sensitive method, instead of the standard maximum-likelihood method, to maximize directly the expected quality of the training set. Experimental results show that CNFpred generates significantly better alignments than the best profile-based and threading methods on several public (but small) benchmarks as well as our own large dataset. CNFpred outperforms others regardless of the lengths or classes of proteins, and works particularly well for proteins with sparse sequence profiles due to the effective utilization of structure information. Our methodology can also be adapted to protein sequence alignment.
Contact: j3xu@ttic.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/bts213
PMCID: PMC3371845  PMID: 22689779
17.  A multiple-template approach to protein threading 
Proteins  2011;79(6):1930-1939.
Most threading methods predict the structure of a protein using only a single template. Due to the increasing number of solved structures, a protein without solved structure is very likely to have more than one similar template structures. Therefore, a natural question to ask is if we can improve modeling accuracy using multiple templates. This paper describes a new multiple-template threading method to answer this question. At the heart of this multiple-template threading method is a novel probabilistic-consistency algorithm that can accurately align a single protein sequence simultaneously to multiple templates. Experimental results indicate that our multiple-template method can improve pairwise sequence-template alignment accuracy and generate models with better quality than single-template models even if they are built from the best single templates (P-value<10-6) while many popular multiple sequence/structure alignment tools fail to do so. The underlying reason is that our probabilistic-consistency algorithm can generate accurate multiple sequence/template alignments. In another word, without an accurate multiple sequence/template alignment the modeling accuracy cannot be improved by simply using multiple templates to increase alignment coverage. Blindly tested on the CASP9 targets with more than one good template structures, our method outperforms all other CASP9 servers except two (Zhang-Server and QUARK of the same group). Our probabilistic-consistency algorithm can possibly be extended to align multiple protein/RNA sequences and structures.
doi:10.1002/prot.23016
PMCID: PMC3092796  PMID: 21465564
protein modeling; multiple-template threading; probabilistic alignment matrix; probabilistic-consistency algorithm; multiple sequence/template alignment
18.  Protein 8-class secondary structure prediction using conditional neural fields 
Proteomics  2011;11(19):3786-3792.
Compared with the protein 3-class secondary structure (SS) prediction, the 8-class prediction gains less attention and is also much more challenging, especially for proteins with few sequence homologs. This paper presents a new probabilistic method for 8-class SS prediction using conditional neural fields (CNFs), a recently invented probabilistic graphical model. This CNF method not only models the complex relationship between sequence features and SS, but also exploits the interdependency among SS types of adjacent residues. In addition to sequence profiles, our method also makes use of non-evolutionary information for SS prediction. Tested on the CB513 and RS126 data sets, our method achieves Q8 accuracy of 64.9 and 64.7%, respectively, which are much better than the SSpro8 web server (51.0 and 48.0%, respectively). Our method can also be used to predict other structure properties (e.g. solvent accessibility) of a protein or the SS of RNA.
doi:10.1002/pmic.201100196
PMCID: PMC3341732  PMID: 21805636
Bioinformatics; Conditional neural fields; Eight class; Protein; Secondary structure prediction
19.  Finding Nearly Optimal GDT Scores 
Journal of Computational Biology  2011;18(5):693-704.
Abstract
Global Distance Test (GDT) is one of the commonly accepted measures to assess the quality of predicted protein structures. Given a set of distance thresholds, GDT maximizes the percentage of superimposed (or matched) residue pairs under each threshold, and reports the average of these percentages as the final score. The computation of GDT score was conjectured to be NP-hard. All available methods are heuristic and do not guarantee the optimality of scores. These heuristic strategies usually result in underestimated GDT scores. Contrary to the conjecture, the problem can be solved exactly in polynomial time, albeit the method would be too slow for practical usage. In this paper we propose an efficient tool called OptGDT to obtain GDT scores with theoretically guaranteed accuracies. Denote ℓ as the number of matched residue pairs found by OptGDT for a given threshold d. Let ℓ′ be the optimal number of matched residues pairs for threshold d/(1 + ε), where ε is a parameter in our computation. OptGDT guarantees that ℓ ≥ ℓ′. We applied our tool to CASP8 (The eighth Critical Assessment of Structure Prediction Techniques) data. For 87.3% of the predicted models, better GDT scores are obtained when OptGDT is used. In some cases, the number of matched residue pairs were improved by at least 10%. The tool runs in time O(n3 log n/ε5) for a given threshold d and parameter ε. In the case of globular proteins, the tool can be improved to a randomized algorithm of O(n log2 n) runtime with probability at least 1 − O(1/n). Released under the GPL license and downloadable from http://bioinformatics.uwaterloo.ca/∼scli/OptGDT/.
doi:10.1089/cmb.2010.0123
PMCID: PMC3607910  PMID: 21554017
algorithms; alignment; computational molecular biology; linear programming; protein folding
20.  Boosting Protein Threading Accuracy 
Protein threading is one of the most successful protein structure prediction methods. Most protein threading methods use a scoring function linearly combining sequence and structure features to measure the quality of a sequence-template alignment so that a dynamic programming algorithm can be used to optimize the scoring function. However, a linear scoring function cannot fully exploit interdependency among features and thus, limits alignment accuracy.
This paper presents a nonlinear scoring function for protein threading, which not only can model interactions among different protein features, but also can be efficiently optimized using a dynamic programming algorithm. We achieve this by modeling the threading problem using a probabilistic graphical model Conditional Random Fields (CRF) and training the model using the gradient tree boosting algorithm. The resultant model is a nonlinear scoring function consisting of a collection of regression trees. Each regression tree models a type of nonlinear relationship among sequence and structure features. Experimental results indicate that this new threading model can effectively leverage weak biological signals and improve both alignment accuracy and fold recognition rate greatly.
doi:10.1007/978-3-642-02008-7_3
PMCID: PMC3325114  PMID: 22506254
protein threading; conditional random fields; gradient tree boosting; regression tree; nonlinear scoring function
21.  A conditional random fields method for RNA sequence–structure relationship modeling and conformation sampling 
Bioinformatics  2011;27(13):i102-i110.
Accurate tertiary structures are very important for the functional study of non-coding RNA molecules. However, predicting RNA tertiary structures is extremely challenging, because of a large conformation space to be explored and lack of an accurate scoring function differentiating the native structure from decoys. The fragment-based conformation sampling method (e.g. FARNA) bears shortcomings that the limited size of a fragment library makes it infeasible to represent all possible conformations well. A recent dynamic Bayesian network method, BARNACLE, overcomes the issue of fragment assembly. In addition, neither of these methods makes use of sequence information in sampling conformations. Here, we present a new probabilistic graphical model, conditional random fields (CRFs), to model RNA sequence–structure relationship, which enables us to accurately estimate the probability of an RNA conformation from sequence. Coupled with a novel tree-guided sampling scheme, our CRF model is then applied to RNA conformation sampling. Experimental results show that our CRF method can model RNA sequence–structure relationship well and sequence information is important for conformation sampling. Our method, named as TreeFolder, generates a much higher percentage of native-like decoys than FARNA and BARNACLE, although we use the same simple energy function as BARNACLE.
Contact: zywang@ttic.edu; j3xu@ttic.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btr232
PMCID: PMC3117333  PMID: 21685058
22.  A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling 
Journal of Computational Biology  2010;17(6):783-798.
Abstract
One of the major challenges with protein template-free modeling is an efficient sampling algorithm that can explore a huge conformation space quickly. The popular fragment assembly method constructs a conformation by stringing together short fragments extracted from the Protein Data Base (PDB). The discrete nature of this method may limit generated conformations to a subspace in which the native fold does not belong. Another worry is that a protein with really new fold may contain some fragments not in the PDB. This article presents a probabilistic model of protein conformational space to overcome the above two limitations. This probabilistic model employs directional statistics to model the distribution of backbone angles and 2nd-order Conditional Random Fields (CRFs) to describe sequence-angle relationship. Using this probabilistic model, we can sample protein conformations in a continuous space, as opposed to the widely used fragment assembly and lattice model methods that work in a discrete space. We show that when coupled with a simple energy function, this probabilistic method compares favorably with the fragment assembly method in the blind CASP8 evaluation, especially on alpha or small beta proteins. To our knowledge, this is the first probabilistic method that can search conformations in a continuous space and achieves favorable performance. Our method also generated three-dimensional (3D) models better than template-based methods for a couple of CASP8 hard targets. The method described in this article can also be applied to protein loop modeling, model refinement, and even RNA tertiary structure prediction.
doi:10.1089/cmb.2009.0235
PMCID: PMC3203516  PMID: 20583926
conditional random fields (CRFs); directional statistics; fragment assembly; lattice model; protein structure prediction; template-free modeling
23.  Low-homology protein threading 
Bioinformatics  2010;26(12):i294-i300.
Motivation: The challenge of template-based modeling lies in the recognition of correct templates and generation of accurate sequence-template alignments. Homologous information has proved to be very powerful in detecting remote homologs, as demonstrated by the state-of-the-art profile-based method HHpred. However, HHpred does not fare well when proteins under consideration are low-homology. A protein is low-homology if we cannot obtain sufficient amount of homologous information for it from existing protein sequence databases.
Results: We present a profile-entropy dependent scoring function for low-homology protein threading. This method will model correlation among various protein features and determine their relative importance according to the amount of homologous information available. When proteins under consideration are low-homology, our method will rely more on structure information; otherwise, homologous information. Experimental results indicate that our threading method greatly outperforms the best profile-based method HHpred and all the top CASP8 servers on low-homology proteins. Tested on the CASP8 hard targets, our threading method is also better than all the top CASP8 servers but slightly worse than Zhang-Server. This is significant considering that Zhang-Server and other top CASP8 servers use a combination of multiple structure-prediction techniques including consensus method, multiple-template modeling, template-free modeling and model refinement while our method is a classical single-template-based threading method without any post-threading refinement.
Contact: jinboxu@gmail.com
doi:10.1093/bioinformatics/btq192
PMCID: PMC2881377  PMID: 20529920
24.  Fragment-free approach to protein folding using conditional neural fields 
Bioinformatics  2010;26(12):i310-i317.
Motivation: One of the major bottlenecks with ab initio protein folding is an effective conformation sampling algorithm that can generate native-like conformations quickly. The popular fragment assembly method generates conformations by restricting the local conformations of a protein to short structural fragments in the PDB. This method may limit conformations to a subspace to which the native fold does not belong because (i) a protein with really new fold may contain some structural fragments not in the PDB and (ii) the discrete nature of fragments may prevent them from building a native-like fold. Previously we have developed a conditional random fields (CRF) method for fragment-free protein folding that can sample conformations in a continuous space and demonstrated that this CRF method compares favorably to the popular fragment assembly method. However, the CRF method is still limited by its capability of generating conformations compatible with a sequence.
Results: We present a new fragment-free approach to protein folding using a recently invented probabilistic graphical model conditional neural fields (CNF). This new CNF method is much more powerful than CRF in modeling the sophisticated protein sequence-structure relationship and thus, enables us to generate native-like conformations more easily. We show that when coupled with a simple energy function and replica exchange Monte Carlo simulation, our CNF method can generate decoys much better than CRF on a variety of test proteins including the CASP8 free-modeling targets. In particular, our CNF method can predict a correct fold for T0496_D1, one of the two CASP8 targets with truly new fold. Our predicted model for T0496 is significantly better than all the CASP8 models.
Contact: jinboxu@gmail.com
doi:10.1093/bioinformatics/btq193
PMCID: PMC2881378  PMID: 20529922
25.  Struct2Net: a web service to predict protein–protein interactions using a structure-based approach 
Nucleic Acids Research  2010;38(Web Server issue):W508-W515.
Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein–protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of the PPI interactome remains inadequate. We believe that Struct2Net is the first community-wide resource to provide structure-based PPI predictions that go beyond homology modeling. Also, most web-resources for predicting PPIs currently rely on functional genomic data (e.g. GO annotation, gene expression, cellular localization, etc.). Our structure-based approach is independent of such methods and only requires the sequence information of the proteins being queried. The web service allows multiple querying options, aimed at maximizing flexibility. For the most commonly studied organisms (fly, human and yeast), predictions have been pre-computed and can be retrieved almost instantaneously. For proteins from other species, users have the option of getting a quick-but-approximate result (using orthology over pre-computed results) or having a full-blown computation performed. The web service is freely available at http://struct2net.csail.mit.edu.
doi:10.1093/nar/gkq481
PMCID: PMC2896152  PMID: 20513650

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