Stefan Richter

TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins

We present TRAPP (TRAnsient Pockets in Proteins), a new automated software platform for tracking, analysis, and visualization of binding pocket variations along a protein motion trajectory or within an ensemble of protein structures that may encompass conformational changes ranging from local side chain fluctuations to global backbone motions. TRAPP performs accurate grid-based calculations of the shape and physicochemical characteristics of a binding pocket for each structure and detects the conserved and transient regions of the pocket in an ensemble of protein conformations. It also provides tools for tracing the opening of a particular subpocket and residues that contribute to the binding site. TRAPP thus enables an assessment of the druggability of a disease-related target protein taking its flexibility into account.

SYCAMORE—a systems biology computational analysis and modeling research environment

UNLABELLEDnSYCAMORE is a browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Thus, it allows e.g. database supported modelling, basic model checking and the estimation of unknown kinetic parameters based on protein structures. In addition, it offers some guidance in order to allow non-expert users to perform basic computational modelling tasks.nnnAVAILABILITYnSYCAMORE is freely available for academic use at http://sycamore.eml.org. Commercial users may acquire a license.nnnCONTACTnursula.kummer@bioquant.uni-heidelberg.de.

SDA 7: A modular and parallel implementation of the simulation of diffusional association software.

The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance.

ProSAT2—Protein Structure Annotation Server

ProSAT2 is a server to facilitate interactive visualization of sequence-based, residue-specific annotations mapped onto 3D protein structures. As the successor of ProSAT (Protein Structure Annotation Tool), it includes its features for visualizing SwissProt and PROSITE functional annotations. Currently, the ProSAT2 server can perform automated mapping of information on variants and mutations from the UniProt KnowledgeBase and the BRENDA enzyme information system onto protein structures. It also accepts and maps user-prepared annotations. By means of an annotation selector, the user can interactively select and group residue-based information according to criteria such as whether a mutation affects enzyme activity. The visualization of the protein structures is based on the WebMol Java molecular viewer and permits simultaneous highlighting of annotated residues and viewing of the corresponding descriptive texts. ProSAT2 is available at .

On the use of PIPSA to guide target-selective drug design.

In structure-based drug design, it is important to design compounds to bind specifically and selectively to their macromolecular target receptor(s). Binding to other macromolecules that are similar to the target may result in adverse side effects and should be avoided. The decision as to which macromolecular target and which region of the target a drug should bind to should therefore include consideration of the binding properties of related macromolecules. Herein, we show how PIPSA (protein interaction property similarity analysis) can aid in surveying the interaction properties of structurally-related macromolecules before embarking on detailed design towards a chosen target site. This is illustrated by application of PIPSA to dihydrofolate reductase (DHFR; EC 1.5.1.3). DHFR is an essential and conserved enzyme in many species. It takes part in folate metabolism and is important for thymidine synthesis. It binds the cofactor NADPH and converts dihydrofolate (DHF) into tetrahydrofolate (THF). As a result of its central role, DHFR is an important drug target and inhibitors, such as methotrexate (MTX), trimethoprim, and pyrimethamine, are used against cancer, bacterial, and parasitic diseases, respectively. A challenge in the application of DHFR inhibitors as antibiotics is the occurrence of side effects. These may arise from the binding of the compounds to human DHFR. On the other hand, it may be advantageous for antibiotics to have a broad spectrum of activity and to bind to several microbial DHFRs. By way of example, we consider herein the selective targeting of compounds to Candida albicans DHFR. Such compounds would be particularly useful to treat common opportunistic infections in immunocompromised patients. Although known clinical drugs against DHFR show weak activity against C. albicans, potent, selective inhibitors of C. albicans DHFR have been reported. Their selectivity for C. albicans versus human DHFR has been ascribed in part to differences in protein–ligand hydrogen bonding. Such differences can be detected by analysis of the protein electrostatic potentials. PIPSA permits quantification of the similarity in the interaction properties of homologous proteins and has been applied to a variety of protein types. PIPSA is available as standalone software but has recently been made available online in the SYCAMORE webserver. In the latter case, it is combined in a workflow with automated protein homology model building and electrostatic potential calculation. Herein, we demonstrate use of the online PIPSA workflow for DHFRs from different species. In the first step of PIPSA, one crystal structure of DHFR (human DHFR, Swiss-Prot identifier P00374) was chosen as a template for homology modeling (Figure 1). All related DHFR

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets

Abstract The TRAnsient Pockets in Proteins (TRAPP) webserver provides an automated workflow that allows users to explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently open due to protein internal motion. These transient or cryptic sub-pockets may be of interest in the design and optimization of small molecular inhibitors for a protein target of interest. The TRAPP workflow consists of the following three modules: (i) TRAPP structure—u2002generation of an ensemble of structures using one or more of four possible molecular simulation methods; (ii) TRAPP analysis—superposition and clustering of the binding site conformations either in an ensemble of structures generated in step (i) or in PDB structures or trajectories uploaded by the user; and (iii) TRAPP pocket—detection, analysis, and visualization of the binding pocket dynamics and characteristics, such as volume, solvent-exposed area or properties of surrounding residues. A standard sequence conservation score per residue or a differential score per residue, for comparing on- and off-targets, can be calculated and displayed on the binding pocket for an uploaded multiple sequence alignment file, and known protein sequence annotations can be displayed simultaneously. The TRAPP webserver is freely available at http://trapp.h-its.org.

LigDig: a web server for querying ligand-protein interactions

Summary: LigDig is a web server designed to answer questions that previously required several independent queries to diverse data sources. It also performs basic manipulations and analyses of the structures of protein–ligand complexes. The LigDig webserver is modular in design and consists of seven tools, which can be used separately, or via linking the output from one tool to the next, in order to answer more complex questions. Currently, the tools allow a user to: (i) perform a free-text compound search, (ii) search for suitable ligands, particularly inhibitors, of a protein and query their interaction network, (iii) search for the likely function of a ligand, (iv) perform a batch search for compound identifiers, (v) find structures of protein–ligand complexes, (vi) compare three-dimensional structures of ligand binding sites and (vii) prepare coordinate files of protein–ligand complexes for further calculations. Availability and implementation: LigDig makes use of freely available databases, including ChEMBL, PubChem and SABIO-RK, and software programs, including cytoscape.js, PDB2PQR, ProBiS and Fconv. LigDig can be used by non-experts in bio- and chemoinformatics. LigDig is available at: http://mcm.h-its.org/ligdig. Contact: jonathan.fuller@h-its.org, rebecca.wade@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.

webSDA: a web server to simulate macromolecular diffusional association

Macromolecular interactions play a crucial role in biological systems. Simulation of diffusional association (SDA) is a software for carrying out Brownian dynamics simulations that can be used to study the interactions between two or more biological macromolecules. webSDA allows users to run Brownian dynamics simulations with SDA to study bimolecular association and encounter complex formation, to compute association rate constants, and to investigate macromolecular crowding using atomically detailed macromolecular structures. webSDA facilitates and automates the use of the SDA software, and offers user-friendly visualization of results. webSDA currently has three modules: ‘SDA docking’ to generate structures of the diffusional encounter complexes of two macromolecules, ‘SDA association’ to calculate bimolecular diffusional association rate constants, and ‘SDA multiple molecules’ to simulate the diffusive motion of hundreds of macromolecules. webSDA is freely available to all users and there is no login requirement. webSDA is available at http://mcm.h-its.org/webSDA/.

ProSAT+: visualizing sequence annotations on 3D structure.

PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org.

Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer

The Dynathor project aims at understanding the interaction of cytochrome P450 (CYP, P450) enzymes and their redox partner, cytochrome P450 reductase (CPR), in a phospholipid bilayer. Through simulation studies on the HLRS CRAY systems (initially XE6, later on XC40), we investigated the interactions of models of membrane-bound P450s (CYP51 and CYP1A1) and CPR. A model of membrane-bound T. brucei CYP51 and the human CPR was successfully built and simulated for 217.5 ns. A model of human CYP1A1 and the human CPR in a phospholipid bilayer was also built and is being simulated. These models can be used as starting points to understand the selectivity of the interactions of CYPs with CPR in the native membrane-bound forms, and thus may aid drug discovery projects.