Drug design tools

Provided by Mind The Byte. Databank of experimentally-determined structures of proteins, nucleic acids, and complex assemblies. Subset of the Protein Data Bank PDB , containing a collection of well resolved protein crystal structures with clearly identified biologically relevant ligands annotated with experimentally determined binding data extracted from literature.

Maintained by the university of Michigan. All of the binding affinity data compiled in this database are cited from original references. A Data Set for Protein-Protein Docking that dentifies and presents protein docking complexes and their unbound structures. They can be used as benchmark sets to develop or to test docking algorithms.

Non-commercial manually curated benchmarking database dedicated to the Nuclear Receptor NR ligands and structures pharmacological profiles. All protonation states have been assigned by manual inspection. It is an extended version of the original GOLD validation test set. Freely accessible database of affinities for protein-ligand complexes from the PDB. Collection of protein ligand complexes extracted fom the PDB along with biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes.

Maintained by the University of Cambridge. Public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. Ki Database. Provides information on the abilities of drugs to interact with an expanding number of molecular targets. The Ki database serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes.

Currently Ki values. Free online repository of protein-ligand complexes which have been structurally resolved and thermodynamically characterised. Psychoactive Drug Screening Program. Provides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters. Assays, K i , BAPPL complexes set. DNA Drug complex dataset. Binding Database. Kuntz Protein Test Set.

Set of crystallographically determined protein-ligand structures used to test the docking program DOCK. Maintained by UCSF. Target databases TTD. Therapeutic Target Database. Database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status.

All information provided are fully referenced. Resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

Small Molecule Pathway Database. Interactive, visual database containing more than small molecule pathways found in humans. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures.

Molecule editor developed by the cheminformatics company CambridgeSoft. For Windows and Mac. Advanced chemical editor for drawing chemical structures, queries and reactions developed by ChemAxon. Exists as an applet. Also available as freeware, with tools for 2D structure cleaning, 3D optimization and viewing, InChI generation and conversion, drawing of polymers, organometallics, and Markush structures.

For Windows only. DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns. Compounds can be clustered and diverse subsets can be picked. Calculated compound similarities can be used for multidimensional scaling methods, e. Kohonen nets. Physicochemical properties can be calculated, structure activity relationship tables can be created and activity cliffs be visualized.

Tool of JChem for clustering, diversity calculations, and library comparisons based on molecular fingerprints and other descriptors. Useful in combinatorial chemistry, drug design, or other areas where a large number of compounds need to be analyzed.

Graphic editing tool for generic chemical patterns. Based on the SMARTS language, chemical patterns can be created and edited interactively, similar to molecule editing in a chemical structure editor. Freely available for linux systems with 32 and 64 bit, windows 32bit systems and MacOS. Developed by the University of Hamburg. Provides features to build a molecule from scratch using 2D Draw and conversion to 3D. The 3D editor allows addition, modification, replacement and deletion of atoms, bonds and groups, with Undo and Redo operations.

Provided by VLife. Free of charge for academic and personal use. Chemical structure environment with a main focus on 2D graphics and publishing to create media for structures, reactions and spectra. For Windows, Mac and Linux. ChemDraw for iPad. Provided by PerkinElmer, Inc. TouchMol Deskop Application. Tool for drawing chemical and biological structures, optimized for Touch Operations. Provides name-to-structure.

For Windows 8. Provided by Scilligence. TouchMol for Office. Desktop tool for drawing chemical and biological structures, into the MS Office suite. ChemDoodle Mobile. Free iPhone companion to ChemDoodle.

ChemDoodle Mobile is a calculator for drawn organic structures. There are four main windows: Draw, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. All spectra are interactive. The Help page contains a thorough help guide. Provided by iChemLabs. Chirys Draw. Application for drawing publication-quality molecular structures and reactions.

Designed from the ground up for the iPad. Developed by Integrated Chemistry Design, Inc. Chirys Sketch. Application for drawing publication-quality molecular structures and reactions, for iPhone and iPod Touch. Mobile Molecular DataSheet. Allows viewing and editing chemical structure diagrams on an iPhone, iPod or iPad.

Molecules are organized in collections of datasheets. Individual molecules, or whole datasheets, can be shared via iTunes or sent by email, using the standard MDL MOL and SDfile formats, which allows the data to be integrated into any external workflow. SAR Table. Structures are represented by scaffolds and substituents, which are combined together to automatically generate a construct molecule.

The table editor has many convenience features and data checking cues to make the data entry process as efficient as possible. Chemical structure drawing tool based on the unique sketcher from the Mobile Molecular DataSheet.

Can send structure data via email, open structures from email or web, create graphical images or Microsoft Word documents with embedded structure graphics, calculate properties based on structures and use structures to search Mobile Reagents and ChemSpider. Portable chemical dataset viewer for iPad, for browsing SAR reports, chemical catalogs, custom-made databases, and physical property references.

Provided by Metamolecular, LLC. Chemistry sketch for iphone and ipad. Developed by Dotmatics Limited. Accelrys Draw. Allows drawing and editing complex molecules, chemical reactions and biological sequences. Program for producing chemical drawings and outputting them in a variety of formats.

For Windows. Free and open source editor and viewer for chemical structures in 2D. Exists as a Java stand alone application and two varieties of Java applet that can be integrated into web pages.

BKChem is a free open source chemical drawing program written in Python. Free open source molecular drawing tool for 2D molecular structures. Available for Windows, Mac and Linux. JME Molecular Editor. Molecular drawing tool. Distributed by ChemInnovation Software. Free open source software program for drawing chemical structural formulas, available for Windows, Unix, and Mac OS. Application that can view, edit and build molecules in 2D.

For iPhone. Free and open source interactive chemical molecule sketching tool, and molecular spreadsheet data entry application.

Written in Java. Can scan all data sources, including local files, remote files on network, emails, web pages, SharePoint contents, etc. Distributed by Scilligence. Toolkit for 2D chemical structure image recognition. Imago is completely free and open-source, while also available on a commercial basis. Java GUI for Imago. Ego is completely free and open-source, while also available on a commercial basis.

Imago Console Application. Command-line interface for Imago. Alter-Ego is completely free and open-source, while also available on a commercial basis. Makes it possible to draw, display and search chemical structures in SharePoint. Molecular drawing software for iPhone. Developed by IDBS. ChemJuice Grande. Molecular drawing software for iPad. Free chemical structure drawing application.

It can draw structures from scratch or load them from ChemSpider and modify them. Structures can be emailed in Molfile format. For Android. DCE ChemPad. Free application to draw chemical structures and calculate molecular weight, molecular formula and to send the molfile. It shows the capabilities of the Dendro Chemical Editor control for Android to build chemistry-aware mobile applications. Command-line molecule and reaction rendering utility. Free and open source.

Distibuted by GGA software. Molecule Editor in JavaScript. Open source. Marvin molecule editor and viewer. Java based chemical editor for drawing chemical structures. Includes unlimited structure based predictions for a range of properties pKa, logD, name structure, etc. Web-based chemical structure editor written in JavaScript. Free and open-source, but also available on a commercial basis.

Chemical structure editor designed for use with Web applications. Distributed by Metamolecular. Allows creation and editing of molecules in browsers without Java support and without any plugins.

The editor is based on a Web2. WebME allows therefore web-based structure input also in institutions where Java applets are not allowed and offers complete platform compatibility. Javascript libary you can display and draw chemical structures in web pages, which works cross browser, including IE, Firefox, Safari, Opera and Chrome, crose platform, including Window, Mac, Linux, and even iPhone, Android and other mobile devices.

Free for education. TouchMol Web. Tool for drawing chemical and biological structure online. Open source, highly extensible program for interactive visualization and analysis of molecular structures and related data. Free of charge for academic, government, non-profit, and personal use.

Open source, user-sponsored, molecular visualization system written in Python. Open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics. Program for 3D visualization of macromolecules, allowing to analyze several proteins at the same time. The VSviewer3D brings together the ability to explore numerical data, such as calculated properties and virtual screening scores, structure depiction, interactive topological and 3D similarity searching, and 3D visualization.

By doing so the user is better able to quickly identify outliers, assess tractability of large numbers of compounds, visualize hits of interest, annotate hits, and mix and match interesting scaffolds. We demonstrate the utility of the VSviewer3D by describing a use case in a docking based virtual screen. Developed by Data2Discovery Consulting Inc. Allows defining binding sites and export to Autodock and VINA input files, doing receptor and ligand preparation automatically, starting docking runs with Autodock or VINA from within the plugin, viewing grid maps generated by autogrid in PyMOL, handling multiple ligands and set up virtual screenings, and set up docking runs with flexible sidechains.

A dehydron calculator plugin for PyMOL. This plugin calculates dehydrons and display them onto the protein structure. It has interfaces to some gromacs functions and uses gromacs routines for command line parsing, reading and writing of structure files pdb,gro, Interactive Python-based interface to the Rosetta molecular modeling suite.

It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions. Free open source molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Developed by the NIH resource for macromolecular modeling and bioinformatics, University of illinois. Free, open-source plug-in that runs molecular modeling software directly inside of professional 3D animation applications hosts, i. Blender, Cinema4D and Maya to provide simultaneous access the capabilities of all of the systems. Developed by the Scripps Research Institute. Open source Java viewer for chemical structures in 3D. Free open source molecular modelling suite for computation, analysis and display of molecular data.

It features state-of-the-art tools for managing molecular databases, run molecular docking experiments, compute raytraced images, etc Developed by Zeden. For windows, Mac and Linux. Internet Explorer is not supported. DS Visualizer. Free 3D visualizer of Discovery Studio. Allows sequence handling and, 2D or 3D charting. Creates 2D ligand-receptor interaction diagrams. Distributed by Accelrys. For Windows and Linux. Free open source java molecular graphics program that assists in structure based drug design.

It can be used as an Applet in a web page or as a desktop application. Provided by Astex Therapeutics. For Windows, linux and Mac. Allows saving interactive 3D files to display on the web or in PowerPoint.

Distributed by Molsoft. For Windows, Mac and linux. Exist in a Pro version. Crystal Studio. It is a comprehensive tool for user-friendly creation, 3D graphical design, display and manipulation of crystal and macro-molecular structures, surface or interfaces and defects and for the simulation of X-Ray, neutron and electron diffraction patterns.

Integrated Front-End application for multiple structure visualization and multiple sequence alignment. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structure alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families.

Friend is also available as an applet. Program for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Free open source program for displaying, analyzing, editing, converting, and animating molecular systems former JMolEditor.

Free molecular visualization program for displaying macromolecules, building molecules, multiple sequence alignments. Open source GPL , interactive, high quality molecular visualization system.

QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins. Free molecular explorer for protein structure visualization, validation and analysis. Mainained by Dr. Nymeyer's Group, Inst.

Program for the macromolecular structure visualization CueMol was formerly called "Que". CueMol aims to visualize the crystallographic models of macromolecules with the user-friendly interfaces. Molecular visualization and computation package. Free and open source software. Visualization tool and graphical user interface of the Chil 2 suite, with analysis tools, database integration and ruby interface. Open for general research. Visualization application and molecular modeling toolkit Molecular mechanics and dynamics, structure-based screening.

Free for non-profit academic uses. Standalone molecular modeling and visualization application. Provides a framework for developing molecular visualization functionality. Can be used as the visualizaion component of BALL. Free and opensource.

Program for molecular graphics visualisation. Free open source molecular visualization software adapted from the program RasMol. RasTop wraps a user-friendly graphical interface around the "RasMol molecular engine". Developed for educational purposes and for the analysis of macromolecules at the bench.

Visualization tool for biomolecular structures, sequences, and sequence alignments. Maintained and distributed by the NCBI.

Free, modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional molecular graphics closely integrated with sequence viewing and sequence alignment editing.

Free software for presentation of molecules. BARISTA visualization functions create, display, and manipulate 3D depictions of molecular structures based on results computed by molecular computation programs such as Conflex, and are designed specifically to facilitate the analysis of these results.

Visualization tool for biomolecular structures and small molecules. Provided by Molsoft. PyMOL on the iPad. High-performance 3D molecular visualizer, designed from the ground up for the iPad. The app enables the general public, researchers and scholars to search the Protein Data Bank and visualize protein structures using either a WiFi or cellular data connection. High-quality molecular visualization app for the iPad, iPhone and iPod Touch. Provided by MolySym. CueMol for iOS. Interactive macromolecular viewer for structural biologists.

Application designed to enable students and professionals to build, construct, modify and examine molecules in 3D. Chem3D for iPad. Chem3D for iPad enables scientists to view and manipulate 3D images of chemical and biochemical structures. Re-imagined for the iPad, the Chem3D app features a facile user interface to manipulate images using common touch, pinch and swipe gestures. Interactive 3D molecular viewer designed specifically for the iPad, iPhone and iPod touch.

CMol allows the user to open and view PDB files with complete control over the representations and colours used for individual chains, residues and atoms. Free application for iPhone and iPad, for viewing three-dimensional renderings of molecules and manipulating them using your fingers. You can rotate the molecules by moving your finger across the display, zoom in or out by using two-finger pinch gestures, or pan the molecule by moving two fingers across the screen at once.

These structures can be viewed in both ball-and-stick and spacefilling visualization modes. The IMoleBuilder is an application that can view, edit and build molecules in 3D. Molecular visualization app for iPad to perform in-silico drug discovery. Hierarchy structure of molecules is shown with a table that select components in a protein and related things. It can generate pharmacophores and analyze 3D protein-ligand interaction of biological macromolecules for in-silico drug discovery.

Allows selecting a ligand from a protein and generate a binding site from the selected ligand. Can generate receptor based pharmacophores and get inspiration. Jmol Molecular Visualization. Free Jmol for Android tablets.

Free molecular viewer for Android. Molecule Viewer 3D. Opens most common 3D molecule file formats saved on a SD card or found in a library of included molecules. Free computational chemistry tool.

Atom 3D. Free application to visualize molecules and crystal structures in 3D using the touchscreen to rotate and zoom. Includes 19 sample structures. Free application for molecular graphics visualization from PDB files. PDB View 3D. Application for molecular graphics visualization from PDB files. It is derived from a structural representation of that substance in a way designed to be independent of the way that the structure was drawn thus a single compound will always produce the same identifier.

Tripos Mol2. Complete description of the Mol2 file format. PDB format. Complete description of the PDB file format. SDF format. Complete description of the SDF file format. File format Converters OpenBabel. Free open source chemical expert system mainly used for converting chemical file formats.

Generates 3D structures for small and medium sized, drug-like molecules. Distributed by Molecular Networks. Universal organic chemistry toolkit, containing tools for end users, as well as a documented API for developers. Command-line program for R-Group deconvolution.

Conformer Ensembles Containing Bioactive Conformations. Converts from 1D or 2D to 3D using distance bounds methods, with a focus on reproducing the bioactive conformation.

Developed by OpenEye. Also exists as a web service. Provided by the University of california, Irvine. Generate and analyse 3D conformers of small molecules. Rules result from statistical analysis of histograms derived from small molecule X-ray data extracted from the CSD.

Rotatable bonds of molecules loaded into the TorsionAnalyzer are color-coded on the fly by means of a traffic light highlighting regular, borderline and unusual torsion angles. This allows the user to see at a glance if one or more torsion angles are out of the ordinary. Provided by BioSolveIT. Distributed by Schrodinger. Universal scriptable toolkit for chemical information processing. Used by PubChem. Maintained and distributed by Xemistry. Free for academic. Optical Structure Recognition Application.

Utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc. Collection of Perl scripts, modules, and classes to support day-to-day computational chemistry needs.

Free software, open source. Provided by Manish Sud. VLife Engine. Engine module of VLifeMDS containing basic molecular modeling capabilities such as building, viewing, editing, modifying, and optimizing small and arge molecules.

Fast conformer generation by systematic and Monte-carlo methods. Structure recognition tool for automated protein and ligand preparation. The protonation can either be done by just adding missing hydrogen atoms or as a complete reprotonation. SPORES is able to generate different protonation states, tautomers and stereoisomers for a given structure.

Developed by the Konstanz university. Freely distributed by the University of Paris Diderot. Molecular modeling tool to convert 2D structures chemical structural formula of compounds drawn by ISIS-Draw or ChemDraw to 3D structures with additional information on atomic charge etc.

Distributed by IMMD. A software suite for drawing chemical structure diagrams, including the ability to calculate NMR spectra, generate IUPAC names and line notations for structures, manipulate structures imported from the Internet, interpret and interconvert files generated by other chemical drawing software programs, illustrate glassware and equipment setups, and draw TLC plates.

Software for searching and analyzing the conformational space of small and large molecules. Cheminformatics library mainly used for conversion of file formats. LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. NET platform. Universal organic chemistry toolkit. Provided by GGA. Open Drug Discovery Toolkit.

It reimplements many state-of-the-art methods, such as machine learning scoring functions RF-Score and NNScore and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible. Therefore, users are strongly encouraged to extend it and develop new methods. Molecule file manipulation and conversion program.

KNOwledge-Driven Ligand Extractor is a software library for the recognition of atomic types, their hybridization states and bond orders in the structures of small molecules. Its prediction model is based on nonlinear Support Vector Machines. The process of bond and atom properties perception is divided into several steps. At the beginning, only information about the coordinates and elements for each atom is available: i Connectivity is recognized; ii A search of rings is performed to find the Smallest Set of Smallest Rings SSSR ; iii Atomic hybridizations are predicted by the corresponding SVM model; iv Bond orders are predicted by the corresponding SVM model; v Aromatic cycles are found and vi Atomic types are set in obedience to the functional groups.

Some bonds are reassigned during this stage. Linux and MacOS version are free of charge. For Mac and Linux. Scaffold Hunter. JAVA-based software tool for exploring the chemical space by enabling generation of and navigation in a scaffold tree hierarchy annotated with various data.

The graphical visualization of structural relationships allows to analyze large data sets, e. Request Sample Schedule a Call. Need immediate assistance? View ToC. Request Sample. Buy Report. Introduction Drug designing tools are computer modeling techniques that provide insights into experimental findings. Request comprehensive report brochure. Sign Up Now. Need specific information? Request Customization. A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis.

Inhibition of 1-deoxy-D-xylulosephosphate reductoisomerase Dxr : a review of the synthesis and biological evaluation of recent inhibitors. Curr Top Med Chem. Crystal structure of 1-deoxy-D-xylulosephosphate reductoisomerase, a crucial enzyme in the non-mevalonate pathway of isoprenoid biosynthesis.

Toward Mycobacterium tuberculosis DXR inhibitor design: homology modeling and molecular dynamics simulations. J Comput Aided Mol Des. The malarial drug target Plasmodium falciparum 1-deoxy-D-xylulosephosphate reductoisomerase PfDXR : development of a 3-D model for identification of novel, structural and functional features and for inhibitor screening.

Protein Pept Lett. Design, synthesis, and X-ray crystallographic studies of alpha-aryl substituted fosmidomycin analogues as inhibitors of Mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase.

Crystallization and preliminary X-ray crystallographic study of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Plasmodium falciparum. Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulosephosphate reductoisomerase provide new insights into catalysis.

Antimalarial and structural studies of pyridine-containing inhibitors of 1-deoxyxylulosephosphate reductoisomerase. Structure-guided design and biosynthesis of a novel FR analogue as a potent Plasmodium falciparum 1-deoxy-D-xylulosephosphate reductoisomerase Dxr inhibitor.

Chem Commun Camb ; 51 13 — Virtual screening of compounds to 1-deoxy-dxylulose 5-phosphate reductoisomerase DXR from Plasmodium falciparum. Alpha-heteroatom derivatized analogues of 3- acetylhydroxyamino propyl phosphonic acid FR as antimalarials. DXR inhibition by potent mono- and disubstituted fosmidomycin analogues. Masini T, Hirsch AK. Development of inhibitors of the 2C-methyl-D-erythritol 4-phosphate MEP pathway enzymes as potential anti-infective agents.

Synthesis and bioactivity of beta-substituted fosmidomycin analogues targeting 1-deoxy-D-xylulosephosphate reductoisomerase. Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment. Source Code Biol Med. Design, synthesis and biological evaluation of quinazoline derivatives as anti-trypanosomatid and anti-plasmodial agents. Eur J Med Chem. A molecular mechanism of artemisinin resistance in Plasmodium falciparum malaria.

Recent progress in the identification and development of anti-malarial agents using virtual screening based approaches. Comb Chem High Throughput Screen. A protein complex network of Drosophila melanogaster. A census of human soluble protein complexes. Wodak SJ, Janin J. Computer analysis of protein-protein interaction. J Mol Biol. A geometric approach to macromolecule-ligand interactions.

CAPRI: a critical assessment of predicted interactions. Critical assessment of methods of protein structure prediction CASP — round x. Assessment of blind predictions of protein-protein interactions: current status of docking methods.

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Protein docking using spherical polar Fourier correlations. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Are scoring functions in protein-protein docking ready to predict interactomes?

Clues from a novel binding affinity benchmark. J Proteome Res. Lensink MF, Mendez R. Recognition-induced conformational changes in protein-protein docking. Curr Pharm Biotechnol. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. May A, Zacharias M. Mustard D, Ritchie DW. Docking essential dynamics eigenstructures.

Implicit flexibility in protein docking: cross-docking and local refinement. Chaudhury S, Gray JJ. Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. Sable R, Jois S. Surfing the protein-protein interaction surface using docking methods: application to the design of PPI inhibitors.

Stabilization of protein-protein interactions in chemical biology and drug discovery. Prog Biophys Mol Biol. From protein communication to drug discovery. In silico design of low molecular weight protein-protein interaction inhibitors: overall concept and recent advances.

Prediction of protein-binding areas by small-world residue networks and application to docking. BMC Bioinformatics. Amino acid network and its scoring application in protein-protein docking. Biophys Chem. Small-world network approach to identify key residues in protein-protein interaction.

Network analysis of protein structures identifies functional residues. Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Comput Biol. Liu R, Hu J. Computational prediction of heme-binding residues by exploiting residue interaction network. J Chem Inf Model.

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Protein-protein docking benchmark 2. Protein-protein docking benchmark version 4. Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol. Drug-like protein-protein interaction modulators: challenges and opportunities for drug discovery and chemical biology. Mol Inform. Hammad N, Jingdong J.

Structure-based protein-protein interaction networks and drug design. Quantitative Biology. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat Biotechnol. Interactome3D: adding structural details to protein networks.

Nat Methods. The topology of drug-target interaction networks: implicit dependence on drug properties and target families. Structure-based systems biology for analyzing off-target binding.

Curr Opin Struct Biol. Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome. Protein hydration dynamics and molecular mechanism of coupled water-protein fluctuations.

Schutz CN, Warshel A. Ben-Naim A. Molecular recognition — viewed through the eyes of the solvent. Bienstock RJ. Solvation methods for protein-ligand docking. Modeling water molecules in protein-ligand docking using GOLD. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock.

Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Recognition between a bacterial ribonuclease, barnase, and its natural inhibitor, barstar. How optimal are the binding energetics of barnase and barstar?

Biophys J. Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2. Adhesive water networks facilitate binding of protein interfaces.

Nat Commun. The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction. Structure of the ultra-high-affinity colicin E2 DNase — Im2 complex.

Transient protein-protein interactions: structural, functional, and network properties. Towards drugs targeting multiple proteins in a systems biology approach.

Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif. Computational assembly of polymorphic amyloid fibrils reveals stable aggregates.

Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Support Center Support Center. External link. Please review our privacy policy.