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1.  MetalionRNA: computational predictor of metal-binding sites in RNA structures 
Bioinformatics  2011;28(2):198-205.
Motivation: Metal ions are essential for the folding of RNA molecules into stable tertiary structures and are often involved in the catalytic activity of ribozymes. However, the positions of metal ions in RNA 3D structures are difficult to determine experimentally. This motivated us to develop a computational predictor of metal ion sites for RNA structures.
Results: We developed a statistical potential for predicting positions of metal ions (magnesium, sodium and potassium), based on the analysis of binding sites in experimentally solved RNA structures. The MetalionRNA program is available as a web server that predicts metal ions for RNA structures submitted by the user.
Availability: The MetalionRNA web server is accessible at http://metalionrna.genesilico.pl/.
Contact: iamb@genesilico.pl
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btr636
PMCID: PMC3259437  PMID: 22110243
2.  NPDock: a web server for protein–nucleic acid docking 
Nucleic Acids Research  2015;43(Web Server issue):W425-W430.
Protein–RNA and protein–DNA interactions play fundamental roles in many biological processes. A detailed understanding of these interactions requires knowledge about protein–nucleic acid complex structures. Because the experimental determination of these complexes is time-consuming and perhaps futile in some instances, we have focused on computational docking methods starting from the separate structures. Docking methods are widely employed to study protein–protein interactions; however, only a few methods have been made available to model protein–nucleic acid complexes. Here, we describe NPDock (Nucleic acid–Protein Docking); a novel web server for predicting complexes of protein–nucleic acid structures which implements a computational workflow that includes docking, scoring of poses, clustering of the best-scored models and refinement of the most promising solutions. The NPDock server provides a user-friendly interface and 3D visualization of the results. The smallest set of input data consists of a protein structure and a DNA or RNA structure in PDB format. Advanced options are available to control specific details of the docking process and obtain intermediate results. The web server is available at http://genesilico.pl/NPDock.
doi:10.1093/nar/gkv493
PMCID: PMC4489298  PMID: 25977296
3.  GeneSilico protein structure prediction meta-server 
Nucleic Acids Research  2003;31(13):3305-3307.
Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta.
PMCID: PMC168964  PMID: 12824313
4.  SimRNAweb: a web server for RNA 3D structure modeling with optional restraints 
Nucleic Acids Research  2016;44(Web Server issue):W315-W319.
RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb.
doi:10.1093/nar/gkw279
PMCID: PMC4987879  PMID: 27095203
5.  COLORADO3D, a web server for the visual analysis of protein structures 
Nucleic Acids Research  2004;32(Web Server issue):W586-W589.
COLORADO3D is a World Wide Web server for the visual presentation of three-dimensional (3D) protein structures. COLORADO3D indicates the presence of potential errors (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), identifies buried residues and depicts sequence conservations. As input, the server takes a file of Protein Data Bank (PDB) coordinates and, optionally, a multiple sequence alignment. As output, the server returns a PDB-formatted file, replacing the B-factor column with values of the chosen parameter (structure quality, residue burial or conservation). Thus, the coordinates of the analyzed protein ‘colored’ by COLORADO3D can be conveniently displayed with structure viewers such as RASMOL in order to visualize the 3D clusters of regions with common features, which may not necessarily be adjacent to each other at the amino acid sequence level. In particular, COLORADO3D may serve as a tool to judge a structure's quality at various stages of the modeling and refinement (during both experimental structure determination and homology modeling). The GeneSilico group used COLORADO3D in the fifth Critical Assessment of Techniques for Protein Structure Prediction (CASP5) to successfully identify well-folded parts of preliminary homology models and to guide the refinement of misthreaded protein sequences. COLORADO3D is freely available for academic use at http://asia.genesilico.pl/colorado3d/.
doi:10.1093/nar/gkh440
PMCID: PMC441578  PMID: 15215456
6.  RIBER/DIBER: a software suite for crystal content analysis in the studies of protein–nucleic acid complexes 
Bioinformatics  2012;28(6):880-881.
Summary: Co-crystallization experiments of proteins with nucleic acids do not guarantee that both components are present in the crystal. We have previously developed DIBER to predict crystal content when protein and DNA are present in the crystallization mix. Here, we present RIBER, which should be used when protein and RNA are in the crystallization drop. The combined RIBER/DIBER suite builds on machine learning techniques to make reliable, quantitative predictions of crystal content for non-expert users and high-throughput crystallography.
Availability: The program source code, Linux binaries and a web server are available at http://diber.iimcb.gov.pl/ RIBER/DIBER requires diffraction data to at least 3.0 Å resolution in MTZ or CIF (web server only) format. The RIBER/DIBER code is subject to the GNU Public License.
Contact: gchojnowski@genesilico.pl
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/bts003
PMCID: PMC3307108  PMID: 22238259
7.  Assessing the Accuracy of Template-Based Structure Prediction Metaservers by Comparison with Structural Genomics Structures 
The explosion of the size of the universe of known protein sequences has stimulated two complementary approaches to structural mapping of these sequences: theoretical structure prediction and experimental determination by structural genomics (SG). In this work, we assess the accuracy of structure prediction by two automated template-based structure prediction metaservers (genesilico.pl and bioinfo.pl) by measuring the structural similarity of the predicted models to corresponding experimental models determined a posteriori. Of 199 targets chosen from SG programs, the metaservers predicted the structures of about a fourth of them “correctly.” (In this case, “correct” was defined as placing more than 70% of the alpha carbon atoms in the model within 2 Å of the experimentally determined positions.) Almost all of the targets that could be modeled to this accuracy were those with an available template in the Protein Data Bank (PDB) with more than 25% sequence identity. The majority of those SG targets with lower sequence identity to structures in the PDB were not predicted by the metaservers with this accuracy. We also compared metaserver results to CASP8 results, finding that the models obtained by participants in the CASP competition were significantly better than those produced by the metaservers.
doi:10.1007/s10969-012-9146-2
PMCID: PMC4105012  PMID: 23086054
8.  pyDockSAXS: protein–protein complex structure by SAXS and computational docking 
Nucleic Acids Research  2015;43(Web Server issue):W356-W361.
Structural characterization of protein–protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques cannot keep pace with current advances in interactomics. Low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be applied at larger scale, but they miss atomic details. For efficient application to protein–protein complexes, low-resolution information can be combined with theoretical methods that provide energetic description and atomic details of the interactions. Here we present the pyDockSAXS web server (http://life.bsc.es/pid/pydocksaxs) that provides an automatic pipeline for modeling the structure of a protein–protein complex from SAXS data. The method uses FTDOCK to generate rigid-body docking models that are subsequently evaluated by a combination of pyDock energy-based scoring function and their capacity to describe SAXS data. The only required input files are structural models for the interacting partners and a SAXS curve. The server automatically provides a series of structural models for the complex, sorted by the pyDockSAXS scoring function. The user can also upload a previously computed set of docking poses, which opens the possibility to filter the docking solutions by potential interface residues or symmetry restraints. The server is freely available to all users without restriction.
doi:10.1093/nar/gkv368
PMCID: PMC4489248  PMID: 25897115
9.  Protein structure prediction guided by cross-linking restraints — A systematic evaluation of the impact of the cross-linking spacer length 
Recent development of high-resolution mass spectrometry (MS) instruments enables chemical cross-linking (XL) to become a high-throughput method for obtaining structural information about proteins. Restraints derived from XL-MS experiments have been used successfully for structure refinement and protein-protein docking. However, one formidable question is under which circumstances XL-MS data might be sufficient to determine a protein’s tertiary structure de novo? Answering this question will not only include understanding the impact of XL-MS data on sampling and scoring within a de novo protein structure prediction algorithm, it must also determine an optimal cross-linker type and length for protein structure determination. Whereas a longer cross-linker will yield more restraints, the value of each restraint for protein structure prediction decreases as the restraint is consistent with a larger conformational space.
In this study, the number of cross-links and their discriminative power was systematically analyzed in silico on a set of 2055 non-redundant protein folds considering Lys-Lys, Lys-Asp, Lys-Glu, Cys-Cys, and Arg-Arg reactive cross-linkers between 1 Å and 60 Å. Depending on the protein size a heuristic was developed that determines the optimal cross-linker length. Next, simulated restraints of variable length were used to de novo predict the tertiary structure of fifteen proteins using the BCL::Fold algorithm. The results demonstrate that a distinct cross-linker length exists for which information content for de novo protein structure prediction is maximized. The sampling accuracy improves on average by 1.0 Å and up to 2.2 Å in the most prominent example. XL-MS restraints enable consistently an improved selection of native-like models with an average enrichment of 2.1.
doi:10.1016/j.ymeth.2015.05.014
PMCID: PMC4803439  PMID: 25986934
10.  FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins 
BMC Bioinformatics  2011;12:160.
Background
The accurate prediction of ligand binding residues from amino acid sequences is important for the automated functional annotation of novel proteins. In the previous two CASP experiments, the most successful methods in the function prediction category were those which used structural superpositions of 3D models and related templates with bound ligands in order to identify putative contacting residues. However, whilst most of this prediction process can be automated, visual inspection and manual adjustments of parameters, such as the distance thresholds used for each target, have often been required to prevent over prediction. Here we describe a novel method FunFOLD, which uses an automatic approach for cluster identification and residue selection. The software provided can easily be integrated into existing fold recognition servers, requiring only a 3D model and list of templates as inputs. A simple web interface is also provided allowing access to non-expert users. The method has been benchmarked against the top servers and manual prediction groups tested at both CASP8 and CASP9.
Results
The FunFOLD method shows a significant improvement over the best available servers and is shown to be competitive with the top manual prediction groups that were tested at CASP8. The FunFOLD method is also competitive with both the top server and manual methods tested at CASP9. When tested using common subsets of targets, the predictions from FunFOLD are shown to achieve a significantly higher mean Matthews Correlation Coefficient (MCC) scores and Binding-site Distance Test (BDT) scores than all server methods that were tested at CASP8. Testing on the CASP9 set showed no statistically significant separation in performance between FunFOLD and the other top server groups tested.
Conclusions
The FunFOLD software is freely available as both a standalone package and a prediction server, providing competitive ligand binding site residue predictions for expert and non-expert users alike. The software provides a new fully automated approach for structure based function prediction using 3D models of proteins.
doi:10.1186/1471-2105-12-160
PMCID: PMC3123233  PMID: 21575183
11.  PSPP: A Protein Structure Prediction Pipeline for Computing Clusters 
PLoS ONE  2009;4(7):e6254.
Background
Protein structures are critical for understanding the mechanisms of biological systems and, subsequently, for drug and vaccine design. Unfortunately, protein sequence data exceed structural data by a factor of more than 200 to 1. This gap can be partially filled by using computational protein structure prediction. While structure prediction Web servers are a notable option, they often restrict the number of sequence queries and/or provide a limited set of prediction methodologies. Therefore, we present a standalone protein structure prediction software package suitable for high-throughput structural genomic applications that performs all three classes of prediction methodologies: comparative modeling, fold recognition, and ab initio. This software can be deployed on a user's own high-performance computing cluster.
Methodology/Principal Findings
The pipeline consists of a Perl core that integrates more than 20 individual software packages and databases, most of which are freely available from other research laboratories. The query protein sequences are first divided into domains either by domain boundary recognition or Bayesian statistics. The structures of the individual domains are then predicted using template-based modeling or ab initio modeling. The predicted models are scored with a statistical potential and an all-atom force field. The top-scoring ab initio models are annotated by structural comparison against the Structural Classification of Proteins (SCOP) fold database. Furthermore, secondary structure, solvent accessibility, transmembrane helices, and structural disorder are predicted. The results are generated in text, tab-delimited, and hypertext markup language (HTML) formats. So far, the pipeline has been used to study viral and bacterial proteomes.
Conclusions
The standalone pipeline that we introduce here, unlike protein structure prediction Web servers, allows users to devote their own computing assets to process a potentially unlimited number of queries as well as perform resource-intensive ab initio structure prediction.
doi:10.1371/journal.pone.0006254
PMCID: PMC2707601  PMID: 19606223
12.  DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking 
BMC Bioinformatics  2011;12:348.
Background
Protein-RNA interactions play fundamental roles in many biological processes. Understanding the molecular mechanism of protein-RNA recognition and formation of protein-RNA complexes is a major challenge in structural biology. Unfortunately, the experimental determination of protein-RNA complexes is tedious and difficult, both by X-ray crystallography and NMR. For many interacting proteins and RNAs the individual structures are available, enabling computational prediction of complex structures by computational docking. However, methods for protein-RNA docking remain scarce, in particular in comparison to the numerous methods for protein-protein docking.
Results
We developed two medium-resolution, knowledge-based potentials for scoring protein-RNA models obtained by docking: the quasi-chemical potential (QUASI-RNP) and the Decoys As the Reference State potential (DARS-RNP). Both potentials use a coarse-grained representation for both RNA and protein molecules and are capable of dealing with RNA structures with posttranscriptionally modified residues. We compared the discriminative power of DARS-RNP and QUASI-RNP for selecting rigid-body docking poses with the potentials previously developed by the Varani and Fernandez groups.
Conclusions
In both bound and unbound docking tests, DARS-RNP showed the highest ability to identify native-like structures. Python implementations of DARS-RNP and QUASI-RNP are freely available for download at http://iimcb.genesilico.pl/RNP/
doi:10.1186/1471-2105-12-348
PMCID: PMC3179970  PMID: 21851628
RNA; protein; RNP; macromolecular docking; complex modeling; structural bioinformatics
13.  Accounting for Observed Small Angle X-ray Scattering Profile in the Protein-Protein Docking Server ClusPro 
Journal of computational chemistry  2015;36(20):1568-1572.
The protein-protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near-native ones for many proteins, selecting the best model is difficult due to the uncertainty in scoring. Small Angle X-ray Scattering (SAXS) is an experimental technique for obtaining low resolution structural information in solution. While not sufficient on its own to uniquely predict complex structures, accounting for SAXS data improves the ranking of models and facilitates the identification of the most accurate structure. Although SAXS profiles are currently available only for a small number of complexes, due to its simplicity the method is becoming increasingly popular. Since combining SAXS experiments will provide a viable strategy for fairly high-throughput determination of protein complex structures, the option of using SAXS restraints is added to the ClusPro server.
doi:10.1002/jcc.23952
PMCID: PMC4485579  PMID: 26095982
protein complex; structure prediction; docking method; scoring function; SAXS restraints
14.  Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction 
PLoS Computational Biology  2015;11(12):e1004661.
Recent work has shown that the accuracy of ab initio structure prediction can be significantly improved by integrating evolutionary information in form of intra-protein residue-residue contacts. Following this seminal result, much effort is put into the improvement of contact predictions. However, there is also a substantial need to develop structure prediction protocols tailored to the type of restraints gained by contact predictions. Here, we present a structure prediction protocol that combines evolutionary information with the resolution-adapted structural recombination approach of Rosetta, called RASREC. Compared to the classic Rosetta ab initio protocol, RASREC achieves improved sampling, better convergence and higher robustness against incorrect distance restraints, making it the ideal sampling strategy for the stated problem. To demonstrate the accuracy of our protocol, we tested the approach on a diverse set of 28 globular proteins. Our method is able to converge for 26 out of the 28 targets and improves the average TM-score of the entire benchmark set from 0.55 to 0.72 when compared to the top ranked models obtained by the EVFold web server using identical contact predictions. Using a smaller benchmark, we furthermore show that the prediction accuracy of our method is only slightly reduced when the contact prediction accuracy is comparatively low. This observation is of special interest for protein sequences that only have a limited number of homologs.
Author Summary
Recently, a breakthrough has been achieved in modeling the atomic 3D structures of proteins from their sequence alone without requiring any experimental work on the protein itself. To achieve this goal, a database of evolutionary related sequences is analyzed to find co-evolving residues, giving insight into which residues are in close proximity to each other. These residue-residue contacts can help to drive a computer simulation with an atomic-scale physical model of the protein structure from a random starting conformation to a native-like 3D conformation. Although much effort is being put into the improvement of residue-residue contact predictions, their accuracy will always be limited. Therefore, structure prediction protocols with a high tolerance against incorrect distance restraints are needed. Here, we present a structure prediction protocol that combines evolutionary information with the iterative sampling approach of the molecular modeling suite Rosetta, called RASREC. RASREC has been shown to converge faster to near-native models and to be more robust against incorrect distance restraints than standard prediction protocols. It is therefore perfectly suited for restraints obtained from predicted residue-residue contacts with limited accuracy. We show that our protocol outperforms other currently published structure prediction methods and is able to achieve accurate structures, even if the accuracy of predicted contacts is low.
doi:10.1371/journal.pcbi.1004661
PMCID: PMC4694711  PMID: 26713437
15.  Distribution and frequencies of post-transcriptional modifications in tRNAs 
RNA Biology  2015;11(12):1619-1629.
Functional tRNA molecules always contain a wide variety of post-transcriptionally modified nucleosides. These modifications stabilize tRNA structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mRNAs during translation. Their presence in functionally important regions of tRNA is conserved in all domains of life. However, the identities of many of these modified residues depend much on the phylogeny of organisms the tRNAs are found in, attesting for domain-specific strategies of tRNA maturation. In this work we present a new tool, tRNAmodviz web server (http://genesilico.pl/trnamodviz) for easy comparative analysis and visualization of modification patterns in individual tRNAs, as well as in groups of selected tRNA sequences. We also present results of comparative analysis of tRNA sequences derived from 7 phylogenetically distinct groups of organisms: Gram-negative bacteria, Gram-positive bacteria, cytosol of eukaryotic single cell organisms, Fungi and Metazoa, cytosol of Viridiplantae, mitochondria, plastids and Euryarchaeota. These data update the study conducted 20 y ago with the tRNA sequences available at that time.
doi:10.4161/15476286.2014.992273
PMCID: PMC4615829  PMID: 25611331
comparative analysis; evolution; modified nucleotides; post-transcriptional modification; RNA maturation; tRNA; tRNA modifications; tRNA sequence; web server
16.  AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction 
Bioinformatics  2015;31(13):2098-2105.
Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available.
Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets.
Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/.
Contact: adam@sanfordburnham.org
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btv092
PMCID: PMC4481839  PMID: 25701568
17.  Structural alignment of protein descriptors – a combinatorial model 
BMC Bioinformatics  2016;17:383.
Background
Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures are nowadays a main premise for understanding the latter. However, computationally derived 3D models often exhibit deviations from the native structure. A way to confirm a model is a comparison with other structures. The structural alignment of a pair of proteins can be defined with the use of a concept of protein descriptors. The protein descriptors are local substructures of protein molecules, which allow us to divide the original problem into a set of subproblems and, consequently, to propose a more efficient algorithmic solution. In the literature, one can find many applications of the descriptors concept that prove its usefulness for insight into protein 3D structures, but the proposed approaches are presented rather from the biological perspective than from the computational or algorithmic point of view. Efficient algorithms for identification and structural comparison of descriptors can become crucial components of methods for structural quality assessment as well as tertiary structure prediction.
Results
In this paper, we propose a new combinatorial model and new polynomial-time algorithms for the structural alignment of descriptors. The model is based on the maximum-size assignment problem, which we define here and prove that it can be solved in polynomial time. We demonstrate suitability of this approach by comparison with an exact backtracking algorithm. Besides a simplification coming from the combinatorial modeling, both on the conceptual and complexity level, we gain with this approach high quality of obtained results, in terms of 3D alignment accuracy and processing efficiency.
Conclusions
All the proposed algorithms were developed and integrated in a computationally efficient tool descs-standalone, which allows the user to identify and structurally compare descriptors of biological molecules, such as proteins and RNAs. Both PDB (Protein Data Bank) and mmCIF (macromolecular Crystallographic Information File) formats are supported. The proposed tool is available as an open source project stored on GitHub (https://github.com/mantczak/descs-standalone).
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-016-1237-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s12859-016-1237-9
PMCID: PMC5027075  PMID: 27639380
Protein structure; Structural comparison; Combinatorial optimization
18.  Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps 
A computer program that builds crystal structure models of nucleic acid molecules is presented. It can be accessed at http://iimcb.genesilico.pl/brickworx.
Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.
doi:10.1107/S1399004715000383
PMCID: PMC4356372  PMID: 25760616
Brickworx; model building; nucleic acids
19.  MODOMICS: a database of RNA modification pathways. 2008 update 
Nucleic Acids Research  2008;37(Database issue):D118-D121.
MODOMICS, a database devoted to the systems biology of RNA modification, has been subjected to substantial improvements. It provides comprehensive information on the chemical structure of modified nucleosides, pathways of their biosynthesis, sequences of RNAs containing these modifications and RNA-modifying enzymes. MODOMICS also provides cross-references to other databases and to literature. In addition to the previously available manually curated tRNA sequences from a few model organisms, we have now included additional tRNAs and rRNAs, and all RNAs with 3D structures in the Nucleic Acid Database, in which modified nucleosides are present. In total, 3460 modified bases in RNA sequences of different organisms have been annotated. New RNA-modifying enzymes have been also added. The current collection of enzymes includes mainly proteins for the model organisms Escherichia coli and Saccharomyces cerevisiae, and is currently being expanded to include proteins from other organisms, in particular Archaea and Homo sapiens. For enzymes with known structures, links are provided to the corresponding Protein Data Bank entries, while for many others homology models have been created. Many new options for database searching and querying have been included. MODOMICS can be accessed at http://genesilico.pl/modomics.
doi:10.1093/nar/gkn710
PMCID: PMC2686465  PMID: 18854352
20.  Protein-Protein Docking with F2Dock 2.0 and GB-Rerank 
PLoS ONE  2013;8(3):e51307.
Motivation
Computational simulation of protein-protein docking can expedite the process of molecular modeling and drug discovery. This paper reports on our new F2 Dock protocol which improves the state of the art in initial stage rigid body exhaustive docking search, scoring and ranking by introducing improvements in the shape-complementarity and electrostatics affinity functions, a new knowledge-based interface propensity term with FFT formulation, a set of novel knowledge-based filters and finally a solvation energy (GBSA) based reranking technique. Our algorithms are based on highly efficient data structures including the dynamic packing grids and octrees which significantly speed up the computations and also provide guaranteed bounds on approximation error.
Results
The improved affinity functions show superior performance compared to their traditional counterparts in finding correct docking poses at higher ranks. We found that the new filters and the GBSA based reranking individually and in combination significantly improve the accuracy of docking predictions with only minor increase in computation time. We compared F2 Dock 2.0 with ZDock 3.0.2 and found improvements over it, specifically among 176 complexes in ZLab Benchmark 4.0, F2 Dock 2.0 finds a near-native solution as the top prediction for 22 complexes; where ZDock 3.0.2 does so for 13 complexes. F2 Dock 2.0 finds a near-native solution within the top 1000 predictions for 106 complexes as opposed to 104 complexes for ZDock 3.0.2. However, there are 17 and 15 complexes where F2 Dock 2.0 finds a solution but ZDock 3.0.2 does not and vice versa; which indicates that the two docking protocols can also complement each other.
Availability
The docking protocol has been implemented as a server with a graphical client (TexMol) which allows the user to manage multiple docking jobs, and visualize the docked poses and interfaces. Both the server and client are available for download. Server: http://www.cs.utexas.edu/~bajaj/cvc/software/f2dock.shtml. Client: http://www.cs.utexas.edu/~bajaj/cvc/software/f2dockclient.shtml.
doi:10.1371/journal.pone.0051307
PMCID: PMC3590208  PMID: 23483883
21.  RNA Bricks—a database of RNA 3D motifs and their interactions 
Nucleic Acids Research  2013;42(Database issue):D123-D131.
The RNA Bricks database (http://iimcb.genesilico.pl/rnabricks), stores information about recurrent RNA 3D motifs and their interactions, found in experimentally determined RNA structures and in RNA–protein complexes. In contrast to other similar tools (RNA 3D Motif Atlas, RNA Frabase, Rloom) RNA motifs, i.e. ‘RNA bricks’ are presented in the molecular environment, in which they were determined, including RNA, protein, metal ions, water molecules and ligands. All nucleotide residues in RNA bricks are annotated with structural quality scores that describe real-space correlation coefficients with the electron density data (if available), backbone geometry and possible steric conflicts, which can be used to identify poorly modeled residues. The database is also equipped with an algorithm for 3D motif search and comparison. The algorithm compares spatial positions of backbone atoms of the user-provided query structure and of stored RNA motifs, without relying on sequence or secondary structure information. This enables the identification of local structural similarities among evolutionarily related and unrelated RNA molecules. Besides, the search utility enables searching ‘RNA bricks’ according to sequence similarity, and makes it possible to identify motifs with modified ribonucleotide residues at specific positions.
doi:10.1093/nar/gkt1084
PMCID: PMC3965019  PMID: 24220091
22.  CONFOLD: Residue-Residue Contact-guided ab initio Protein Folding 
Proteins  2015;83(8):1436-1449.
Predicted protein residue-residue contacts can be used to build three-dimensional models and consequently to predict protein folds from scratch. A considerable amount of effort is currently being spent to improve contact prediction accuracy, whereas few methods are available to construct protein tertiary structures from predicted contacts. Here, we present an ab initio protein folding method to build three-dimensional models using predicted contacts and secondary structures. Our method first translates contacts and secondary structures into distance, dihedral angle and hydrogen bond restraints according to a set of new conversion rules, and then provides these restraints as input for a distance geometry algorithm to build tertiary structure models. The initially reconstructed models are used to regenerate a set of physically realistic contact restraints and detect secondary structure patterns, which are then used to reconstruct final structural models. This unique two-stage modeling approach of integrating contacts and secondary structures improves the quality and accuracy of structural models and in particular generates better β-sheets than other algorithms. We validate our method on two standard benchmark datasets using true contacts and secondary structures. Our method improves TM-score of reconstructed protein models by 45% and 42% over the existing method on the two datasets respectively. On the dataset for benchmarking reconstruction methods with predicted contacts and secondary structures, the average TM-score of best models reconstructed by our method is 0.59, 5.5% higher than the existing method. The CONFOLD web server is available at http://protein.rnet.missouri.edu/confold/.
doi:10.1002/prot.24829
PMCID: PMC4509844  PMID: 25974172
Protein residue-residue contacts; protein structure modeling; ab initio protein folding; contact assisted protein structure prediction; optimization
23.  CING: an integrated residue-based structure validation program suite 
Journal of Biomolecular Nmr  2012;54(3):267-283.
We present a suite of programs, named CING for Common Interface for NMR Structure Generation that provides for a residue-based, integrated validation of the structural NMR ensemble in conjunction with the experimental restraints and other input data. External validation programs and new internal validation routines compare the NMR-derived models with empirical data, measured chemical shifts, distance- and dihedral restraints and the results are visualized in a dynamic Web 2.0 report. A red–orange–green score is used for residues and restraints to direct the user to those critiques that warrant further investigation. Overall green scores below ~20 % accompanied by red scores over ~50 % are strongly indicative of poorly modelled structures. The publically accessible, secure iCing webserver (https://nmr.le.ac.uk) allows individual users to upload the NMR data and run a CING validation analysis.
Electronic supplementary material
The online version of this article (doi:10.1007/s10858-012-9669-7) contains supplementary material, which is available to authorized users.
doi:10.1007/s10858-012-9669-7
PMCID: PMC3483101  PMID: 22986687
NMR; Structure validation; PDB; Errors; Quality; Protein structure
24.  Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution 
Recent developments in PHENIX are reported that allow the use of reference-model torsion restraints, secondary-structure hydrogen-bond restraints and Ramachandran restraints for improved macromolecular refinement in phenix.refine at low resolution.
Traditional methods for macromolecular refinement often have limited success at low resolution (3.0–3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine. Firstly, a ‘reference-model’ method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a ϕ,ψ term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from non­redundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered R free and a decreased gap between R work and R free.
doi:10.1107/S0907444911047834
PMCID: PMC3322597  PMID: 22505258
macromolecular crystallography; low resolution; refinement; automation
25.  Automated 3D structure composition for large RNAs 
Nucleic Acids Research  2012;40(14):e112.
Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.
doi:10.1093/nar/gks339
PMCID: PMC3413140  PMID: 22539264

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