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1.  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
2.  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
3.  ThreaDom: extracting protein domain boundary information from multiple threading alignments 
Bioinformatics  2013;29(13):i247-i256.
Motivation: Protein domains are subunits that can fold and evolve independently. Identification of domain boundary locations is often the first step in protein folding and function annotations. Most of the current methods deduce domain boundaries by sequence-based analysis, which has low accuracy. There is no efficient method for predicting discontinuous domains that consist of segments from separated sequence regions. As template-based methods are most efficient for protein 3D structure modeling, combining multiple threading alignment information should increase the accuracy and reliability of computational domain predictions.
Result: We developed a new protein domain predictor, ThreaDom, which deduces domain boundary locations based on multiple threading alignments. The core of the method development is the derivation of a domain conservation score that combines information from template domain structures and terminal and internal alignment gaps. Tested on 630 non-redundant sequences, without using homologous templates, ThreaDom generates correct single- and multi-domain classifications in 81% of cases, where 78% have the domain linker assigned within ±20 residues. In a second test on 486 proteins with discontinuous domains, ThreaDom achieves an average precision 84% and recall 65% in domain boundary prediction. Finally, ThreaDom was examined on 56 targets from CASP8 and had a domain overlap rate 73, 87 and 85% with the target for Free Modeling, Hard multiple-domain and discontinuous domain proteins, respectively, which are significantly higher than most domain predictors in the CASP8. Similar results were achieved on the targets from the most recently CASP9 and CASP10 experiments.
Availability: http://zhanglab.ccmb.med.umich.edu/ThreaDom/.
Contact: zhng@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btt209
PMCID: PMC3694664  PMID: 23812990
4.  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
5.  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
6.  Recognizing Protein Substructure Similarity Using Segmental Threading 
Summary
Protein template identification is essential to protein structure and function predictions. However, conventional whole-chain threading approaches often fail to recognize conserved substructure motifs when the target and templates do not share the same fold. We develop a new approach, SEGMER, for identifying protein substructure similarities by segmental threading. The target sequence is split into segments of 2–4 consecutive or non-consecutive secondary structural elements, which are then threaded through PDB to identify appropriate substructure motifs. SEGMER is tested on 144 non-redundant hard proteins. When combined with whole-chain threading, the TM-score of alignments and accuracy of spatial restraints of SEGMER increase by 16% and 25%, respectively, compared to that by the whole-chain threading methods only. When tested on 12 Free Modeling targets from CASP8, SEGMER increases the TM-score and contact accuracy by 28% and 48%, respectively. This significant improvement should have important impact on protein structure modeling and functional inference.
doi:10.1016/j.str.2010.04.007
PMCID: PMC2908588  PMID: 20637422
protein structure prediction; segmental threading; contact restraints
7.  BioShell-Threading: versatile Monte Carlo package for protein 3D threading 
BMC Bioinformatics  2014;15:22.
Background
The comparative modeling approach to protein structure prediction inherently relies on a template structure. Before building a model such a template protein has to be found and aligned with the query sequence. Any error made on this stage may dramatically affects the quality of result. There is a need, therefore, to develop accurate and sensitive alignment protocols.
Results
BioShell threading software is a versatile tool for aligning protein structures, protein sequences or sequence profiles and query sequences to a template structures. The software is also capable of sub-optimal alignment generation. It can be executed as an application from the UNIX command line, or as a set of Java classes called from a script or a Java application. The implemented Monte Carlo search engine greatly facilitates the development and benchmarking of new alignment scoring schemes even when the functions exhibit non-deterministic polynomial-time complexity.
Conclusions
Numerical experiments indicate that the new threading application offers template detection abilities and provides much better alignments than other methods. The package along with documentation and examples is available at: http://bioshell.pl/threading3d.
doi:10.1186/1471-2105-15-22
PMCID: PMC3937128  PMID: 24444459
8.  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
9.  LOMETS: A local meta-threading-server for protein structure prediction 
Nucleic Acids Research  2007;35(10):3375-3382.
We developed LOMETS, a local threading meta-server, for quick and automated predictions of protein tertiary structures and spatial constraints. Nine state-of-the-art threading programs are installed and run in a local computer cluster, which ensure the quick generation of initial threading alignments compared with traditional remote-server-based meta-servers. Consensus models are generated from the top predictions of the component-threading servers, which are at least 7% more accurate than the best individual servers based on TM-score at a t-test significance level of 0.1%. Moreover, side-chain and C-alpha (Cα) contacts of 42 and 61% accuracy respectively, as well as long- and short-range distant maps, are automatically constructed from the threading alignments. These data can be easily used as constraints to guide the ab initio procedures such as TASSER for further protein tertiary structure modeling. The LOMETS server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/LOMETS.
doi:10.1093/nar/gkm251
PMCID: PMC1904280  PMID: 17478507
10.  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
11.  eThread: A Highly Optimized Machine Learning-Based Approach to Meta-Threading and the Modeling of Protein Tertiary Structures 
PLoS ONE  2012;7(11):e50200.
Template-based modeling that employs various meta-threading techniques is currently the most accurate, and consequently the most commonly used, approach for protein structure prediction. Despite the evident progress in this field, accurate structure models cannot be constructed for a significant fraction of gene products, thus the development of new algorithms is required. Here, we describe the development, optimization and large-scale benchmarking of eThread, a highly accurate meta-threading procedure for the identification of structural templates and the construction of corresponding target-to-template alignments. eThread integrates ten state-of-the-art threading/fold recognition algorithms in a local environment and extensively uses various machine learning techniques to carry out fully automated template-based protein structure modeling. Tertiary structure prediction employs two protocols based on widely used modeling algorithms: Modeller and TASSER-Lite. As a part of eThread, we also developed eContact, which is a Bayesian classifier for the prediction of inter-residue contacts and eRank, which effectively ranks generated multiple protein models and provides reliable confidence estimates as structure quality assessment. Excluding closely related templates from the modeling process, eThread generates models, which are correct at the fold level, for >80% of the targets; 40–50% of the constructed models are of a very high quality, which would be considered accurate at the family level. Furthermore, in large-scale benchmarking, we compare the performance of eThread to several alternative methods commonly used in protein structure prediction. Finally, we estimate the upper bound for this type of approach and discuss the directions towards further improvements.
doi:10.1371/journal.pone.0050200
PMCID: PMC3503980  PMID: 23185577
12.  Template-based protein structure modeling using TASSERVMT 
Proteins  2011;10.1002/prot.23183.
Template-based protein structure modeling is commonly used for protein structure prediction. Based on the observation that multiple template-based methods often perform better than single template-based methods, we further explore the use of a variable number of multiple templates for a given target in the latest variant of TASSER, TASSERVMT. We first develop an algorithm that improves the target-template alignment for a given template. The improved alignment, called the SP3 alternative alignment, is generated by a parametric alignment method coupled with short TASSER refinement on models selected using knowledge-based scores. The refined top model is then structurally aligned to the template to produce the SP3 alternative alignment. Templates identified using SP3 threading are combined with the SP3 alternative and HHEARCH alignments to provide target alignments to each template. These template models are then grouped into sets containing a variable number of template/alignment combinations. For each set, we run short TASSER simulations to build full-length models. Then, the models from all sets of templates are pooled, and the top 20–50 models selected using FTCOM ranking method. These models are then subjected to a single longer TASSER refinement run for final prediction. We benchmarked our method by comparison with our previously developed approach, pro-sp3-TASSER, on a set with 874 Easy and 318 Hard targets. The average GDT-TS score improvements for the first model are 3.5% and 4.3% for Easy and Hard targets, respectively. When tested on the 112 CASP9 targets, our method improves the average GDT-TS scores as compared to pro-sp3-TASSER by 8.2% and 9.3% for the 80 Easy and 32 Hard targets, respectively. It also shows slightly better results than the top ranked CASP9 Zhang-Server, QUARK and HHpredA methods. The program is available for download at http://cssb.biology.gatech.edu/.
doi:10.1002/prot.23183
PMCID: PMC3291807  PMID: 22105797
template-based modeling; threading; alignment; SP3; TASSER
13.  A comprehensive assessment of sequence-based and template-based methods for protein contact prediction 
Bioinformatics (Oxford, England)  2008;24(7):924-931.
Motivation
Pair-wise residue-residue contacts in proteins can be predicted from both threading templates and sequence-based machine learning. However, most structure modeling approaches only use the template-based contact predictions in guiding the simulations; this is partly because the sequence-based contact predictions are usually considered to be less accurate than that by threading. With the rapid progress in sequence databases and machine-learning techniques, it is necessary to have a detailed and comprehensive assessment of the contact-prediction methods in different template conditions.
Results
We develop two methods for protein-contact predictions: SVM-SEQ is a sequence-based machine learning approach which trains a variety of sequence-derived features on contact maps; SVM-LOMETS collects consensus contact predictions from multiple threading templates. We test both methods on the same set of 554 proteins which are categorized into ‘Easy’, ‘Medium’, ‘Hard’ and ‘Very Hard’ targets based on the evolutionary and structural distance between templates and targets. For the Easy and Medium targets, SVM-LOMETS obviously outperforms SVM-SEQ; but for the Hard and Very Hard targets, the accuracy of the SVM-SEQ predictions is higher than that of SVM-LOMETS by 12–25%. If we combine the SVM-SEQ and SVM-LOMETS predictions together, the total number of correctly predicted contacts in the Hard proteins will increase by more than 60% (or 70% for the long-range contact with a sequence separation ≥24), compared with SVM-LOMETS alone. The advantage of SVM-SEQ is also shown in the CASP7 free modeling targets where the SVM-SEQ is around four times more accurate than SVM-LOMETS in the long-range contact prediction. These data demonstrate that the state-of-the-art sequence-based contact prediction has reached a level which may be helpful in assisting tertiary structure modeling for the targets which do not have close structure templates. The maximum yield should be obtained by the combination of both sequence- and template-based predictions.
doi:10.1093/bioinformatics/btn069
PMCID: PMC2648832  PMID: 18296462
14.  TASSER_low-zsc: An approach to improve structure prediction using low z-score ranked templates 
Proteins  2010;78(13):2769-2780.
In a variety of threading methods, often poorly ranked (low z-score) templates have good alignments. Here, a new method, TASSER_low-zsc that identifies these low z-score ranked templates to improve protein structure prediction accuracy is described. The approach consists of clustering of threading templates by affinity propagation on the basis of structural similarity (thread_cluster) followed by TASSER modeling, with final models selected using a TASSER_QA variant. To establish generality of the approach, templates provided by two threading methods, SP3 and SPARKS2, are examined. The SP3 and SPARKS2 benchmark datasets consist of 351 and 357 medium/hard proteins (those with moderate to poor quality templates and/or alignments) of length ≤ 250 residues respectively. For SP3 medium and hard targets, using thread_cluster, the TM-scores of the best template improve by ~4% and ~9% over the original set (without low z-score templates) respectively; after TASSER modeling/refinement and ranking, the best model improves by ~7% and ~9% over the best model generated with the original template set. Moreover, TASSER_low-zsc generates 22% (43%) more foldable medium (hard) targets. Similar improvements are observed with low ranked templates from SPARKS2. The template clustering approach could be applied to other modeling methods that utilize multiple templates to improve structure prediction.
doi:10.1002/prot.22791
PMCID: PMC2927721  PMID: 20635423
Structure prediction; threading; TASSER; tertiary structure
15.  Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices 
Nucleic Acids Research  2004;32(Web Server issue):W532-W535.
Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms. The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure. A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles.
doi:10.1093/nar/gkh357
PMCID: PMC441495  PMID: 15215443
16.  Incorporating Ab Initio energy into threading approaches for protein structure prediction 
BMC Bioinformatics  2011;12(Suppl 1):S54.
Background
Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches—threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in Ab Initio methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the Ab Initio energy function can be used to improve threading, especially for the weakly/distant homologous templates.
Results
In this paper, we investigate the possibility to improve alignment-generating through incorporating distant interaction information into the alignment scoring function in a nontrivial approach. Specifically, the distant interaction information is introduced through employing an Ab Initio energy function to evaluate the “partial” decoy built from an alignment. Subsequently, a local search algorithm is utilized to optimize the scoring function.
Experimental results demonstrate that with distant interaction items, the quality of generated alignments are improved on 68 out of 127 query-template pairs in Prosup benchmark. In addition, compared with state-to-art threading methods, our method performs better on alignment accuracy comparison.
Conclusions
Incorporating Ab Initio energy functions into threading can greatly improve alignment accuracy.
doi:10.1186/1471-2105-12-S1-S54
PMCID: PMC3044312  PMID: 21342587
17.  Template-based and free modeling by RAPTOR++ in CASP8 
Proteins  2009;77(Suppl 9):133-137.
We developed and tested RAPTOR++ in CASP8 for protein structure prediction. RAPTOR++ contains four modules: threading, model quality assessment, multiple protein alignment and template-free modeling. RAPTOR++ first threads a target protein to all the templates using three methods and then predicts the quality of the 3D model implied by each alignment using a model quality assessment method. Based upon the predicted quality, RAPTOR++ employs different strategies as follows. If multiple alignments have good quality, RAPTOR++ builds a multiple protein alignment between the target and top templates and then generates a 3D model using MODELLER. If all the alignments have very low quality, RAPTOR++ uses template-free modeling. Otherwise, RAPTOR++ submits a threading-generated 3D model with the best quality. RAPTOR++ was not ready for the first 1/3 targets and was under development during the whole CASP8 season. The template-based and template-free modeling modules in RAPTOR++ are not closely integrated. We are using our template-free modeling technique to refine template-based models.
doi:10.1002/prot.22567
PMCID: PMC2785131  PMID: 19722267
template-based modeling; template-free modeling; protein threading; model quality assessment
18.  A Protocol for Computer-Based Protein Structure and Function Prediction 
Genome sequencing projects have ciphered millions of protein sequence, which require knowledge of their structure and function to improve the understanding of their biological role. Although experimental methods can provide detailed information for a small fraction of these proteins, computational modeling is needed for the majority of protein molecules which are experimentally uncharacterized. The I-TASSER server is an on-line workbench for high-resolution modeling of protein structure and function. Given a protein sequence, a typical output from the I-TASSER server includes secondary structure prediction, predicted solvent accessibility of each residue, homologous template proteins detected by threading and structure alignments, up to five full-length tertiary structural models, and structure-based functional annotations for enzyme classification, Gene Ontology terms and protein-ligand binding sites. All the predictions are tagged with a confidence score which tells how accurate the predictions are without knowing the experimental data. To facilitate the special requests of end users, the server provides channels to accept user-specified inter-residue distance and contact maps to interactively change the I-TASSER modeling; it also allows users to specify any proteins as template, or to exclude any template proteins during the structure assembly simulations. The structural information could be collected by the users based on experimental evidences or biological insights with the purpose of improving the quality of I-TASSER predictions. The server was evaluated as the best programs for protein structure and function predictions in the recent community-wide CASP experiments. There are currently >20,000 registered scientists from over 100 countries who are using the on-line I-TASSER server.
doi:10.3791/3259
PMCID: PMC3308591  PMID: 22082966
19.  Improving threading algorithms for remote homology modeling by combining fragment and template comparisons 
Proteins  2010;78(9):2041-2048.
In this work, we develop a method called FTCOM for assessing the global quality of protein structural models for targets of medium and hard difficulty (remote homology) produced by structure prediction approaches such as threading or ab initio structure prediction. FTCOM requires the Cα coordinates of full length models and assesses model quality based on fragment comparison and a score derived from comparison of the model to top threading templates. On a set of 361 medium/hard targets, FTCOM was applied to and assessed for its ability to improve upon the results from the SP3, SPARKS, PROSPECTOR_3, and PRO-SP3-TASSER threading algorithms. The average TM-score improves by 5%–10% for the first selected model by the new method over models obtained by the original selection procedure in the respective threading methods. Moreover the number of foldable targets (TM-score ≥0.4) increases from least 7.6% for SP3 to 54% for SPARKS. Thus, FTCOM is a promising approach to template selection.
doi:10.1002/prot.22717
PMCID: PMC2868272  PMID: 20455261
protein structure prediction; threading; quality assessment prediction; SP3; PROSPECTOR; SPARKS; PRO-SP3-TASSER
20.  Using Structure to Explore the Sequence Alignment Space of Remote Homologs 
PLoS Computational Biology  2011;7(10):e1002175.
Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is “optimal” in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are “suboptimal” in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for “modelability”, we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.
Author Summary
It has been suggested that, for nearly every protein sequence, there is already a protein with a similar structure in current protein structure databases. However, with poor or undetectable sequence relationships, it is expected that accurate alignments and models cannot be generated. Here we show that this is not the case, and that whenever structural relationship exists, there are usually local sequence relationships that can be used to generate an accurate alignment, no matter what the global sequence identity. However, this requires an alternative to the traditional dynamic programming algorithm and the consideration of a small ensemble of alignments. We present an algorithm, S4, and demonstrate that it is capable of generating accurate alignments in nearly all cases where a structural relationship exists between two proteins. Our results thus constitute an important advance in the full exploitation of the information in structural databases. That is, the expectation of an accurate alignment suggests that a meaningful model can be generated for nearly every sequence for which a suitable template exists.
doi:10.1371/journal.pcbi.1002175
PMCID: PMC3188491  PMID: 21998567
21.  Protein-protein complex structure predictions by multimeric threading and template recombination 
Summary
The number of protein-protein complex structures is nearly 6-times smaller than that of tertiary structures in PDB which limits the power of homology-based approaches to complex structure modeling. We present a new threading-recombination approach, COTH, to boost the protein complex structure library by combining tertiary structure templates with complex alignments. The query sequences are first aligned to complex templates using a modified dynamic programming algorithm, guided by ab initio binding-site predictions. The monomer alignments are then shifted to the multimeric template framework by structural alignments. COTH was tested on 500 non-homologous dimeric proteins, which can successfully detect correct templates for half of the cases after homologous templates are excluded, which significantly outperforms conventional homology modeling algorithms. It also shows a higher accuracy in interface modeling than rigid-body docking of unbound structures from ZDOCK although with lower coverage. These data demonstrate new avenues to model complex structures from non-homologous templates.
doi:10.1016/j.str.2011.04.006
PMCID: PMC3134792  PMID: 21742262
Protein-protein docking; protein structure prediction; protein complex recognition
22.  Vorescore—fold recognition improved by rescoring of protein structure models 
Bioinformatics  2010;26(18):i474-i481.
Summary: The identification of good protein structure models and their appropriate ranking is a crucial problem in structure prediction and fold recognition. For many alignment methods, rescoring of alignment-induced models using structural information can improve the separation of useful and less useful models as compared with the alignment score. Vorescore, a template-based protein structure model rescoring system is introduced. The method scores the model structure against the template used for the modeling using Vorolign. The method works on models from different alignment methods and incorporates both knowledge from the prediction method and the rescoring.
Results: The performance of Vorescore is evaluated in a large-scale and difficult protein structure prediction context. We use different threading methods to create models for 410 targets, in three scenarios: (i) family members are contained in the template set; (ii) superfamily members (but no family members); and (iii) only fold members (but no family or superfamily members). In all cases Vorescore improves significantly (e.g. 40% on both Gotoh and HHalign at the fold level) on the model quality, and clearly outperforms the state-of-the-art physics-based model scoring system Rosetta. Moreover, Vorescore improves on other successful rescoring approaches such as Pcons and ProQ. In an additional experiment we add high-quality models based on structural alignments to the set, which allows Vorescore to improve the fold recognition rate by another 50%.
Availability: All models of the test set (about 2 million, 44 GB gzipped) are available upon request.
Contact: csaba@bio.ifi.lmu.de; ralf.zimmer@ifi.lmu.de
doi:10.1093/bioinformatics/btq369
PMCID: PMC2935407  PMID: 20823310
23.  iWRAP: An interface threading approach with application to prediction of cancer related protein-protein interactions 
Journal of molecular biology  2010;405(5):1295-1310.
Current homology modeling methods for predicting protein-protein interactions (PPIs) have difficulty in the “twilight zone” (<40%) of sequence identities. Threading methods extend coverage further into the twilight zone by aligning primary sequences for a pair of proteins to a best-fit template complex to predict an entire three-dimensional structure. We introduce a threading approach, iWRAP, which focuses on only the protein interface. Our approach combines a novel linear programming formulation for interface alignment with a boosting classifier for interaction prediction. We demonstrate its efficacy on SCOPPI, a classification of PPIs in the Protein Databank, and on the entire yeast genome. iWRAP provides significantly improved prediction of PPIs and their interfaces in stringent cross-validation on SCOPPI. Furthermore, by combining our predictions with a full-complex threader, we achieve coverage of 13% for the yeast PPIs, which is close to a 50% increase over previous methods at a higher sensitivity. As an application, we effectively combine iWRAP with genomic data to identify novel cancer related genes involved in chromatin remodeling, nucleosome organization and ribonuclear complex assembly. iWRAP is available at http://iwrap.csail.mit.edu.
doi:10.1016/j.jmb.2010.11.025
PMCID: PMC3028939  PMID: 21130772
structural bioinformatics; protein-protein interactions; threading; cancer; genome annotation
24.  FINDSITEX: A structure based, small molecule virtual screening approach with application to all identified human GPCRs 
Molecular Pharmaceutics  2012;9(6):1775-1784.
We have developed FINDSITEX, an extension of FINDSITE, a protein threading based algorithm for the inference of protein binding sites, biochemical function and virtual ligand screening, that removes the limitation that holo protein structures (those containing bound ligands) of a sufficiently large set of distant evolutionarily related proteins to the target be solved; rather, predicted protein structures and experimental ligand binding information are employed. To provide the predicted protein structures, a fast and accurate version of our recently developed TASSERVMT, TASSERVMT-lite, for template-based protein structural modeling applicable up to 1000 residues is developed and tested, with comparable performance to the top CASP9 servers. Then, a hybrid approach that combines structure alignments with an evolutionary similarity score for identifying functional relationships between target and proteins with binding data has been developed. By way of illustration, FINDSITEX is applied to 998 identified human G-protein coupled receptors (GPCRs). First, TASSERVMT-lite provides updates of all human GPCR structures previously modeled in our lab. We then use these structures and the new function similarity detection algorithm to screen all human GPCRs against the ZINC8 non-redundant (TC<0.7) ligand set combined with ligands from the GLIDA database (a total of 88,949 compounds). Testing (excluding GPCRs whose sequence identity > 30% to the target from the binding data library) on a 168 human GPCR set with known binding data, the average enrichment factor in the top 1% of the compound library (EF0.01) is 22.7, whereas EF0.01 by FINDSITE is 7.1. For virtual screening when just the target and its native ligands are excluded, then the average EF0.01 reaches 41.4. We also analyze off-target interactions for the 168 protein test set. All predicted structures, virtual screening data and off-target interactions for the 998 human GPCRs are available at http://cssb.biology.gatech.edu/skolnick/webservice/gpcr/index.html.
doi:10.1021/mp3000716
PMCID: PMC3396429  PMID: 22574683
TASSERVMT; FINDSITE; GPCR modeling; template-based modeling; virtual screening
25.  Incorporation of Local Structural Preference Potential Improves Fold Recognition 
PLoS ONE  2011;6(2):e17215.
Fold recognition, or threading, is a popular protein structure modeling approach that uses known structure templates to build structures for those of unknown. The key to the success of fold recognition methods lies in the proper integration of sequence, physiochemical and structural information. Here we introduce another type of information, local structural preference potentials of 3-residue and 9-residue fragments, for fold recognition. By combining the two local structural preference potentials with the widely used sequence profile, secondary structure information and hydrophobic score, we have developed a new threading method called FR-t5 (fold recognition by use of 5 terms). In benchmark testings, we have found the consideration of local structural preference potentials in FR-t5 not only greatly enhances the alignment accuracy and recognition sensitivity, but also significantly improves the quality of prediction models.
doi:10.1371/journal.pone.0017215
PMCID: PMC3041821  PMID: 21365008

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