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1.  PROSESS: a protein structure evaluation suite and server 
Nucleic Acids Research  2010;38(Web Server issue):W633-W640.
PROSESS (PROtein Structure Evaluation Suite and Server) is a web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy or computational modeling. While many structure evaluation packages have been developed over the past 20 years, PROSESS is unique in its comprehensiveness, its capacity to evaluate X-ray, NMR and predicted structures as well as its ability to evaluate a variety of experimental NMR data. PROSESS integrates a variety of previously developed, well-known and thoroughly tested methods to evaluate both global and residue specific: (i) covalent and geometric quality; (ii) non-bonded/packing quality; (iii) torsion angle quality; (iv) chemical shift quality and (v) NOE quality. In particular, PROSESS uses VADAR for coordinate, packing, H-bond, secondary structure and geometric analysis, GeNMR for calculating folding, threading and solvent energetics, ShiftX for calculating chemical shift correlations, RCI for correlating structure mobility to chemical shift and PREDITOR for calculating torsion angle-chemical shifts agreement. PROSESS also incorporates several other programs including MolProbity to assess atomic clashes, Xplor-NIH to identify and quantify NOE restraint violations and NAMD to assess structure energetics. PROSESS produces detailed tables, explanations, structural images and graphs that summarize the results and compare them to values observed in high-quality or high-resolution protein structures. Using a simplified red–amber–green coloring scheme PROSESS also alerts users about both general and residue-specific structural problems. PROSESS is intended to serve as a tool that can be used by structure biologists as well as database curators to assess and validate newly determined protein structures. PROSESS is freely available at
PMCID: PMC2896095  PMID: 20460469
2.  MolProbity: all-atom contacts and structure validation for proteins and nucleic acids 
Nucleic Acids Research  2007;35(Web Server issue):W375-W383.
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at
PMCID: PMC1933162  PMID: 17452350
3.  STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins 
Nucleic Acids Research  2004;32(Web Server issue):W500-W502.
STRIDE is a software tool for secondary structure assignment from atomic resolution protein structures. It implements a knowledge-based algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignments in maximal agreement with crystallographers' designations. The STRIDE web server provides access to this tool and allows visualization of the secondary structure, as well as contact and Ramachandran maps for any file uploaded by the user with atomic coordinates in the Protein Data Bank (PDB) format. A searchable database of STRIDE assignments for the latest PDB release is also provided. The STRIDE server is accessible from
PMCID: PMC441567  PMID: 15215436
4.  The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli 
Nucleic Acids Research  2004;32(Database issue):D293-D295.
The CyberCell Database (CCDB: is a comprehensive, web-accessible database designed to support and coordinate international efforts in modeling an Escherichia coli cell on a computer. The CCDB brings together both observed and derived quantitative data from numerous independent sources covering many aspects of the genomic, proteomic and metabolomic character of E.coli (strain K12). The database is self-updating but also supports ‘community’ annotation, and provides an extensive array of viewing, querying and search options including a powerful, easy-to-use relational data extraction system.
PMCID: PMC308842  PMID: 14681416
5.  Gaia: automated quality assessment of protein structure models 
Bioinformatics  2011;27(16):2209-2215.
Motivation: Increasing use of structural modeling for understanding structure–function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures.
Results: In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement.
Availability and Implementation: We provide these tools that appraise protein structures in the form of a web server Gaia ( Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3150034  PMID: 21700672
6.  In silico prediction of exposure amino acid sequences of outer inflammatory protein A of Helicobacter pylori for surface display on Eschierchia coli 
Outer inflammatory protein A (OipA) is an outer membrane protein of Helicobacter pylori that is involved in inducing IL-8 and intracellular signaling. In this study, we have predicted exposure amino acid sequences of OipA for insertion in permissive sites of CstH subunit of Eschierchia coli CS3 pilli for bacterial surface display.
Databases: National Center for Biotechnology Institute and Protein Data Bank. Servers: PHD, SABLE, GOR 4, SignalP3.0, TBBpred, PRODIV-TMHMM, TMRPres2D, CPH Models, PHYRE, GETAREA, VADAR, Pep state and pep window. Software: Swiss PDB viewer and Discovery studio.
In silico prediction of exposure amino acid sequences of OipA led to detection of six sequences of amino acid, 76-87, 106-112, 170-182, 222-230, 242-258, and 278-290. These sequences inserted between amino acid sequences 66-67, 100-101, and 109-110 of CstH that were predicted by Eskandari et al. as permissive sites of CstH.
OipA has the ability to induce IL-8 from gastric epithelial cells and some papers are mentioned that this outer membrane protein involve to attachment and intracellular signaling. Receptor of OipA and adhesion motifs on this protein is unknown. Detection of exposure motifs aids to recognition of adhesion motifs and receptor of OipA on gastric epithelial cells. In this study, we have predicted exposure amino acid sequences for insert to subunit CstH of CS3 pilli E. coli for surface display.
PMCID: PMC3385185  PMID: 22754227
CstH; in silico prediction; OipA; surface sequences
7.  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
PMCID: PMC441578  PMID: 15215456
8.  HARMONY: a server for the assessment of protein structures 
Nucleic Acids Research  2006;34(Web Server issue):W231-W234.
Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (φ,ψ) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at
PMCID: PMC1538917  PMID: 16844999
9.  PRince: a web server for structural and physicochemical analysis of Protein-RNA interface 
Nucleic Acids Research  2012;40(Web Server issue):W440-W444.
We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein–RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in ‘.pdb’ format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein–RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein–RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein–RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at
PMCID: PMC3394290  PMID: 22689640
10.  Phosfinder: a web server for the identification of phosphate-binding sites on protein structures 
Nucleic Acids Research  2011;39(Web Server issue):W278-W282.
Phosfinder is a web server for the identification of phosphate binding sites in protein structures. Phosfinder uses a structural comparison algorithm to scan a query structure against a set of known 3D phosphate binding motifs. Whenever a structural similarity between the query protein and a phosphate binding motif is detected, the phosphate bound by the known motif is added to the protein structure thus representing a putative phosphate binding site. Predicted binding sites are then evaluated according to (i) their position with respect to the query protein solvent-excluded surface and (ii) the conservation of the binding residues in the protein family. The server accepts as input either the PDB code of the protein to be analyzed or a user-submitted structure in PDB format. All the search parameters are user modifiable. Phosfinder outputs a list of predicted binding sites with detailed information about their structural similarity with known phosphate binding motifs, and the conservation of the residues involved. A graphical applet allows the user to visualize the predicted binding sites on the query protein structure. The results on a set of 52 apo/holo structure pairs show that the performance of our method is largely unaffected by ligand-induced conformational changes. Phosfinder is available at
PMCID: PMC3125782  PMID: 21622655
11.  FlexPred: a web-server for predicting residue positions involved in conformational switches in proteins 
Bioinformation  2008;3(3):134-136.
Conformational switches observed in the protein backbone play a key role in a variety of fundamental biological activities. This paper describes a web-server that implements a pattern recognition algorithm trained on the examples from the Database of Macromolecular Movements to predict residue positions involved in conformational switches. Prediction can be performed at an adjustable false positive rate using a user-supplied protein sequence in FASTA format or a structure in a Protein Data Bank (PDB) file. If a protein sequence is submitted, then the web-server uses sequence-derived information only (such as evolutionary conservation of residue positions). If a PDB file is submitted, then the web-server uses sequence-derived information and residue solvent accessibility calculated from this file.
FlexPred is publicly available at
PMCID: PMC2639688  PMID: 19238251
conformational variability; support vector machine; protein flexibility; structural transition; prediction
12.  DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry 
Nucleic Acids Research  2012;40(Web Server issue):W249-W256.
DR_bind is a web server that automatically predicts DNA-binding residues, given the respective protein structure based on (i) electrostatics, (ii) evolution and (iii) geometry. In contrast to machine-learning methods, DR_bind does not require a training data set or any parameters. It predicts DNA-binding residues by detecting a cluster of conserved, solvent-accessible residues that are electrostatically stabilized upon mutation to Asp−/Glu−. The server requires as input the DNA-binding protein structure in PDB format and outputs a downloadable text file of the predicted DNA-binding residues, a 3D visualization of the predicted residues highlighted in the given protein structure, and a downloadable PyMol script for visualization of the results. Calibration on 83 and 55 non-redundant DNA-bound and DNA-free protein structures yielded a DNA-binding residue prediction accuracy/precision of 90/47% and 88/42%, respectively. Since DR_bind does not require any training using protein–DNA complex structures, it may predict DNA-binding residues in novel structures of DNA-binding proteins resulting from structural genomics projects with no conservation data. The DR_bind server is freely available with no login requirement at
PMCID: PMC3394278  PMID: 22661576
13.  Super: a web server to rapidly screen superposable oligopeptide fragments from the protein data bank 
Nucleic Acids Research  2012;40(Web Server issue):W334-W339.
Searching for well-fitting 3D oligopeptide fragments within a large collection of protein structures is an important task central to many analyses involving protein structures. This article reports a new web server, Super, dedicated to the task of rapidly screening the protein data bank (PDB) to identify all fragments that superpose with a query under a prespecified threshold of root-mean-square deviation (RMSD). Super relies on efficiently computing a mathematical bound on the commonly used structural similarity measure, RMSD of superposition. This allows the server to filter out a large proportion of fragments that are unrelated to the query; >99% of the total number of fragments in some cases. For a typical query, Super scans the current PDB containing over 80 500 structures (with ∼40 million potential oligopeptide fragments to match) in under a minute. Super web server is freely accessible from:
PMCID: PMC3394326  PMID: 22638586
14.  PepBuild: a web server for building structure data of peptides/proteins 
Nucleic Acids Research  2004;32(Web Server issue):W559-W561.
PepBuild, a web server, will aid in designing and building a capped or uncapped peptide/protein with known secondary and tertiary structure. The user can build a peptide/protein by choosing the required amino acid residue with regular secondary structure. The torsional angles can be supplied by the user, if desired. The server also allows the user to add relevant protecting groups at the N- and/or C-terminal of the peptide. The amino acid side chains of the designed peptide are optimized using rotameric libraries. Finally, the server provides the option of displaying the result or downloading the complete file in PDB (Protein Data Bank) format. This PDB file can later be used as an input for various molecular simulation programs or for graphical display. The web server is available at
PMCID: PMC441610  PMID: 15215449
15.  3dSS: 3D structural superposition 
Nucleic Acids Research  2006;34(Web Server issue):W128-W132.
3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several 3D protein structures. In addition, the server can be effectively used to find the invariant and common water molecules present in the superposed homologous protein structures. The molecular visualization tool RASMOL is interfaced with the server to visualize the superposed 3D structures with the water molecules (invariant or common) in the client machine. Furthermore, an option is provided to save the superposed 3D atomic coordinates in the client machine. To perform the above, users need to enter Protein Data Bank (PDB)-id(s) or upload the atomic coordinates in PDB format. This server uses a locally maintained PDB anonymous FTP server that is being updated weekly. This program can be accessed through our Bioinformatics web server at the URL or .
PMCID: PMC1538824  PMID: 16844975
16.  ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins 
Nucleic Acids Research  2012;40(Web Server issue):W214-W221.
The ProBiS web server is a web server for detection of structurally similar binding sites in the PDB and for local pairwise alignment of protein structures. In this article, we present a new version of the ProBiS web server that is 10 times faster than earlier versions, due to the efficient parallelization of the ProBiS algorithm, which now allows significantly faster comparison of a protein query against the PDB and reduces the calculation time for scanning the entire PDB from hours to minutes. It also features new web services, and an improved user interface. In addition, the new web server is united with the ProBiS-Database and thus provides instant access to pre-calculated protein similarity profiles for over 29 000 non-redundant protein structures. The ProBiS web server is particularly adept at detection of secondary binding sites in proteins. It is freely available at, and the new ProBiS web server is at
PMCID: PMC3394329  PMID: 22600737
17.  pdbFun: mass selection and fast comparison of annotated PDB residues 
Nucleic Acids Research  2005;33(Web Server issue):W133-W137.
pdbFun () is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. Users can select any residue subset (even including any number of PDB structures) by combining the available features. Selections can be used as probe and target in multiple structure comparison searches. For example a search could involve, as a query, all solvent-exposed, hydrophylic residues that are not in alpha-helices and are involved in nucleotide binding. Possible examples of targets are represented by another selection, a single structure or a dataset composed of many structures. The output is a list of aligned structural matches offered in tabular and also graphical format.
PMCID: PMC1160259  PMID: 15980442
18.  KINARI-Web: a server for protein rigidity analysis 
Nucleic Acids Research  2011;39(Web Server issue):W177-W183.
KINARI-Web is an interactive web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, adding hydrogen atoms and identifying stabilizing interactions. KINARI-Web offers a quick-start option for beginners, and highly customizable features for the experienced user. Chains, residues or atoms, as well as stabilizing constraints can be selected, removed or added, and the user can designate how different chemical interactions should be modeled during rigidity analysis. The enhanced Jmol-based visualizer allows for zooming in, highlighting or investigating different calculated rigidity properties of a molecular structure. KINARI-Web is freely available at
PMCID: PMC3125808  PMID: 21693559
19.  WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures 
Bioinformatics  2013;29(20):2649-2650.
Summary: The understanding of the biological role of RNA molecules has changed. Although it is widely accepted that RNAs play important regulatory roles without necessarily coding for proteins, the functions of many of these non-coding RNAs are unknown. Thus, determining or modeling the 3D structure of RNA molecules as well as assessing their accuracy and stability has become of great importance for characterizing their functional activity. Here, we introduce a new web application, WebRASP, that uses knowledge-based potentials for scoring RNA structures based on distance-dependent pairwise atomic interactions. This web server allows the users to upload a structure in PDB format, select several options to visualize the structure and calculate the energy profile. The server contains online help, tutorials and links to other related resources. We believe this server will be a useful tool for predicting and assessing the quality of RNA 3D structures.
Availability and implementation: The web server is available at It has been tested on the most popular web browsers and requires Java plugin for Jmol visualization.
PMCID: PMC3789544  PMID: 23929030
20.  DECOMP: A PDB decomposition tool on the web 
Bioinformation  2009;3(10):413-414.
The protein databank (PDB) contains high quality structural data for computational structural biology investigations. We have earlier described a fast tool (the decomp_pdb tool) for identifying and marking missing atoms and residues in PDB files. The tool also automatically decomposes PDB entries into separate files describing ligands and polypeptide chains. Here, we describe a web interface named DECOMP for the tool. Our program correctly identifies multi­monomer ligands, and the server also offers the preprocessed ligand­protein decomposition of the complete PDB for downloading (up to size: 5GB)
PMCID: PMC2737496  PMID: 19759860
PDB; web tool; decomposition; server; ligands; SEQRES
21.  HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures 
Nucleic Acids Research  2008;36(Web Server issue):W185-W189.
As protein–protein interactions are crucial in most biological processes, it is valuable to understand how and where protein pairs interact. We developed a web server HOMCOS (Homology Modeling of Complex Structure, to predict interacting protein pairs and interacting sites by homology modeling of complex structures. Our server is capable of three services. The first is modeling heterodimers from two query amino acid sequences posted by users. The server performs BLAST searches to identify homologous templates in the latest representative dataset of heterodimer structures generated from the PQS database. Structure validity is evaluated by the combination of sequence similarity and knowledge-based contact potential energy as previously described. The server generates a sequence-replaced model PDB file and a MODELLER script to build full atomic models of complex structures. The second service is modeling homodimers from one query sequence. The third service is identification of potentially interacting proteins for one query sequence. The server searches the dataset of heterodimer structures for a homologous template, outputs the candidate interacting sequences in the Uniprot database homologous for the interacting partner template proteins. These features are useful for wide range of researchers to predict putative interaction sites and interacting proteins.
PMCID: PMC2447736  PMID: 18442990
22.  PRTAD: A Database for Protein Residue Torsion Angle Distributions 
PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modeling. The database is developed to host and analyze the statistical data for protein residue level “virtual” bond and torsion angles obtained from their distributions in databases of known protein structures such as in the PDB Data Bank. PRTAD is capable of generating, caching, and displaying the statistical distributions of the angles of various types. The collected information can be used to extract geometric restraints or define statistical potentials for protein structure determination. PRTAD is supported with a friendly designed web interface so that users can easily specify the angle types, and retrieve, visualize, or download the distributions of the angles as they desire. The database PRTAD is freely accessible at
PMCID: PMC3018885  PMID: 20052908
Protein structural databases; structural refinement and analysis; protein geometric properties; virtual bond lengths and angles; statistical potentials
23.  PESDserv: a server for high-throughput comparison of protein binding site surfaces 
Bioinformatics  2010;26(15):1913-1914.
Summary: Structure-based approaches complement ligand-based approaches for lead-discovery and cross-reactivity prediction. We present to the scientific community a web server for comparing the surface of a ligand bound site of a protein against a ligand bound site surface database of 106 796 sites. The web server implements the property encoded shape distributions (PESD) algorithm for surface comparison. A typical virtual screen takes 5 min to complete. The output provides a ranked list of sites (by site similarity), hyperlinked to the corresponding entries in the PDB and PDBeChem databases.
Availability: The server is freely accessible at
PMCID: PMC2905548  PMID: 20538727
24.  Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials 
BMC Bioinformatics  2010;11:92.
Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online.
Our new knowledge-based potential server makes available many of these potentials for easy use to automatically compute the energies of protein structures or models supplied. Our web server for protein energy estimation uses four-body potentials, short-range potentials, and 23 different two-body potentials. Users can select potentials according to their needs and preferences. Files containing the coordinates of protein atoms in the PDB format can be uploaded as input. The results will be returned to the user's email address.
Our Potentials 'R'Us server is an easily accessible, freely available tool with a web interface that collects all existing and future protein coarse-grained potentials and computes energies of multiple structural models.
PMCID: PMC3098114  PMID: 20163737
25.  3dLOGO: a web server for the identification, analysis and use of conserved protein substructures 
Nucleic Acids Research  2007;35(Web Server issue):W416-W419.
3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at
PMCID: PMC1933223  PMID: 17488847

Results 1-25 (749203)