3DMSS-Sites provides means to search for 3D sub structures between structures. The search is general: 3DMSS-Sites searches for similar "clouds" of coordinates between sets of coordinates, i.e it is independent on the order of the atoms of the structures. Atomic or residue type compatibilities can be defined to avoid non relevant pairings.
Pairwise and multiple identification of three-dimensional common substructures in proteins.
J Comput Biol. 1998 Spring;5(1):41-56.
Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm.
Comput. Chem. 1998;22(6):463-5.
AMMOS is a software platform that employs an automatic procedure for energy minimization of protein-ligands complexes via the website AMMOS2 and of small chemical compounds via the website AMMOS. AMMOS offers valuable solutions to assist structure-based in silico screening experiments or ligand-based projects.
AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.
Nucleic Acids Res. 2017 May 9.
Post-docking optimization of protein-ligand interactions involving water molecules.
Asian J Physics. 2014;23:745-56.
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening.
BMC Bioinformatics. 2008 Oct 16;9:438.
BactPepDB is a database of predicted peptides from an exhaustive survey of complete prokaryote genomes. It provides insights about candidate peptides, and provides information about their conservation, together with some of their expected biological/structural features. The BactPepDB interface allows to search for candidate peptides in the database, or to search for peptides similar to a query, according to the multiple properties predicted or related to genomic localization.
BactPepDB: a database of predicted peptides from an exhaustive survey of complete prokaryote genomes.
Database (Oxford). 2014 Nov 6;2014. Print 2014.
BCSearch is a fast and flexible approach to identify linear fragments similar to a query in large collections of structures. It addresses two basic questions:
BCSearch is based on a new similarity approach, based on a Binet Cauchy (BC) kernel. The approach measures the correlation between the volumes of all the tetraedron of the query and that of a target. The similarity (BCscore) is scored between -1 and 1, where a value of 1 corresponds to the exact same conformation than the query, and -1 to the mirror conformation. Values close to 0 correspond to unrelated fragments. The BCscore is more stringent than other criteria such as the alpha carbon RMS deviation. Particularly, fragments with partly dissimilar shapes are poorly scored and consequently collections of matches are usually less noisy, which makes them better suited for the analysis of the local structure-sequence relationship. In addition, since no superimposition is required, the similarity search is very fast, making possible to mine large collections of structures.
BCSearch: fast structural fragment mining over large collections of protein structures.
Nucleic Acids Res. 2015 Jul 1;43(W1):W378-82.
FAF-Drugs (Free ADME-Tox Filtering Tool version 4.0) is a program for filtering large compound libraries prior to in silico screening experiments or related modeling studies. The main goal is the computational prediction of some ADME-Tox properties (Adsorption, Distribution, Metabolism, Excretion and Toxicity) in order to assist hit selection before chemical synthesis or ordering.
FAF-Drugs employs pre-defined filters, but users can also customize their own filtering parameters by using the Filter-Editor service.
FAF-Drugs3: a web server for compound property calculation and chemical library design.
Nucleic Acids Res. 2015 Jul 1;43(W1):W200-7.
The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections.
Bioinformatics. 2011 Jul 15;27(14):2018-20.
FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects
BMC Bioinformatics. 2008 Sep 24;9:396.
fpocket is a very fast, open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program, and from now as a web server too.
Since its first release, the new package mdpocket has been developped. This package has been designed to track cavities on different, aligned protein structures, and thus can be used to:
Currently available as a web server only, mdpocket will be released in the fpocket official distribution as soon as the corresponding scientific paper will be published.
fpocket: online tools for protein ensemble pocket detection and tracking.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W582-9.
Fpocket: An open source platform for ligand pocket detection.
BMC Bioinformatics. 2009 Jun 2;10:168.
Frog is intended to generate 3D for drugs, usually described using a 1D or 2D representation. Frog performs isomer identification from ambiguous compound description. Frog is able to generate multi-conformations per isomer.
Frog2: Efficient 3D conformation ensemble generator for small compounds.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W622-7.
Frog: a FRee Online druG 3D conformation generator.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W568-72.
HHalign-Kbest is useful to automatically obtain optimized alignments and models in case of low sequence identity (<35%) between a query and a template protein. It can generate k suboptimal (e.g. top-k scoring) alignments rather than only the optimal one which may contain small to large errors.
HHalign-KBest: exploring sub-optimal alignments for remote homology comparative modeling
Bioinformatics. 2015 Dec 1;31(23):3850-2.
InterEvDock is a server for protein docking running the InterEvScore potential specifically designed to integrate evolutionary information in the docking process. The InterEvScore potential was developed for heteromeric protein interfaces and combines a residue-based multi-body statistical potential with evolutionary information derived from the multiple sequence alignments of each partner in the complex.
InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information.
Nucleic Acids Res. 2016 Jul 8;44(W1):W542-9.
InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution.
Bioinformatics. 2013 29(14):1742-9.
iSuperpose performs the 3D superposition of protein structures by best superimposing the alpha-carbons (or the backbone) of the proteins given a alignment specifying the correspondence between the structures. If no alignment is provided, a structural alignment will be calculated using TMalign. One the alignement is identified, the superposition is achieved using a quaternion based procedure using a specific eigen value calculation implementation. See QBestFit.
MIR is a program that allows to determine residues involved in the core of proteins. A Monte Carlo algorithm is used to simulate the early steps of protein folding and the mean number of neighbours is calculated after 10 steps. Residues surrounded by many others may play a role in the compactness of the protein and thus are called Most Interacting Residues (MIR).
Protein intrachain contact prediction with most interacting residues (MIR).
Bio-Algorithms and Med-Systems 2014 Nov 27;10(4):227-242
Analysis of fragments induced by simulated lattice protein folding.
C R Biol. 2004 May;327(5):431-43.
Universal positions in globular proteins.
Eur J Biochem. 2004 Dec;271(23-24):4762-8.
Open screening endeavors play and will play key role in order to facilitate the identification of new bioactive compounds for drug discovery and chemical biology purposes. Such open access tools are critical to advance the success of drug discovery projects in particular for academic groups.
MTiAutoDock and MTiOpenScreen are two services dedicated to small molecule docking and chemical library virtual screening.
MTiOpenScreen: a web server for structure-based virtual screening.
Nucleic Acids Res. 2015 Jul 1;43(W1):W448-54.
PatchSearch allows local nonsequential searching for similar regions, called patches, on protein surfaces. It is based on detection of quasi-cliques in product graphs representing all the possible matchings between a patch and compared structures.
PatchSearch: A Fast Computational Method for Off-Target Detection.
J Chem Inf Model. 2017 Apr 24;57(4):769-777.
Fast protein fragment similarity scoring using a Binet-Cauchy kernel.
Bioinformatics. 2014 Mar 15;30(6):784-91.
PCE performs the calculation of the electrostatic potentials for a protein by solving numerically the Poisson-Boltzmann equation (the Finite Difference Poisson- Boltzmann method, FDPB). It is a server adaptation of the MEAD potential program (MEAD: Macroscopic Electrostatics with Atomic Detail, D. Bashford).
Two types of services are currently proposed: electrostatic potentials calculation and pKa calculations.
PCE: web tools to compute Protein Continuum Electrostatics.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W372-5.
pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. Nevertheless, its performance is similar or better than state-of-the-art local docking protocols that do require binding site information.
Here we present a Web server for pepATTRACT, carrying out only the rigid-body stage of the protocol, performing docking runs in about 10 minutes. Combined with the fact that it is fully blind, this makes the Web server well-suited for proteome-wide in silico protein-peptide docking experiments.
The pepATTRACT web server for blind, large-scale peptide-protein docking.
Nucleic Acids Res. 2017 Apr 29.
PEP-FOLD is a de novo approach aimed at predicting peptide structures from amino acid sequences.
This method, based on structural alphabet SA letters to describe the conformations of four consecutive residues, couples the predicted series of SA letters to a greedy algorithm and a coarse-grained force field.
PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex.
Nucleic Acids Res. 2016 Jul 8;44(W1):W449-54.
Improved PEP-FOLD approach for peptide and miniprotein structure prediction
J. Chem. Theor. Comput. 2014; 10:4745-4758
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W288-93.
A fast and accurate method for large-scale de novo peptide structure prediction.
J Comput Chem. 2010 Mar;31(4):726-38.
PEP-FOLD: an online resource for de novo peptide structure prediction.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W498-503.
PEP-SiteFinder is a service aimed at identifying patches on a protein surface, which a peptide of specified sequence is likely to interact with.
PEP-SiteFinder: a tool for the blind indentification of peptide binding sites on protein surfaces.
Nucleic Acids Res. 2014 May 6.
The Protein Picture Generator is a service that aims to provide an easy way to generate pictures and movies of protein structures, with the concern of integrating the most frequently used concepts of the molecular graphics fields via the software Dino. High definition pictures and movies are produced via the use of the Megapov engine founded on the Persistance of Vision Ray tracer - POV-Ray engine. This rendering engine is coupled with external programs such as stride (secondary structure determination), or msms (molecular surface calculation). This service can produce static images as well as movies illustrating macromolecular "docking", molecular dynamics, NMR model diversity and protein motions (from http://molmovdb.mbb.yale.edu/)..
PMG: online generation of high-quality molecular pictures and storyboarded animations.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W483-8.
The Protein Picture Generator is a simple tool to generate, given a protein structure file (PDB format), a picture of it.
The ProPHet program combines a coarse-grain / elastic network (ENM) protein model and a Brownian Dynamics algorithm to compute protein local rigidity on the residue level.
The program uses a PDB structural file as a starting point and will produce a rigidity profile of the protein under study with a force constant value for each residue in the protein.
Motions and mechanics: investigating conformational transitions in multi-domain proteins with coarse-grain simulations.
Mol. Simul. 2014, 229-236.
SABBAC is an on-line service devoted to protein backbone reconstruction from alpha-carbon trace. It is based on the assembly of fragments issued from library of reduced size, resulting from the encoding of the protein trace in an HMM-derived structural alphabet. The assembly of the fragments is achieved by a greedy algorithm, using an energy based scoring inspired from the OPEP force field. Alpha-carbon coordinates remain unaffected. SABBAC simply positions the missing backbone atoms, no further refinement is performed. From our tests, SABBAC performs equal or better than other similar online approach and is robust to deviations on the alpha-carbon coordinates.
SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W147-51.
SA-Frag is a service that will, given an amino acid sequence, return 3D fragments predicted to match the various positions of the sequence. SA-Frag will thus return an alignement of the fragments identified with the query and a collection of 3D structures corresponding to the fragments in the PDB format.
Detecting protein candidate fragments using a structural alphabet profile comparison approach.
PLoS One. 2013 Nov 26;8(11)
SolyPep is a fast and flexible random sequence generator for producing peptides selected for their aqueous solubility
The server first generates the required number peptides of desired length. This input library can alternatively be provided by the user in fasta format by pasting the sequences in the input field or by uploading a file. Each peptide sequence can be filtered according to a set of simple rules designed to guarantee the peptide solubility. The next step of the service will offer the processing of individual peptide sequences into 3D coordinates, files for use direct in autodock or vina can optionnally be added to the archive. It is important to note that the 3D generation step aims at providing starting conformations for flexible docking using a tool such as autodock, not predicting the conformation of the peptides in solution.
SolyPep: a fast generator of soluble peptides
SPROUTS has been designed to give scientists access to data related to protein folding prediction. In this scope, we processed a set of proteins on five different tools devoted to the prediction of stability changes upon point mutation. We also propose the results obtained with two methods devoted for one to the direct prediction of residues involved in the core of a protein structure and for the other, the characterization of fragments which ends are assumed to be part of the folding nucleus.
SPROUTS: a database for the evaluation of protein stability upon point mutation.
Nucleic Acids Res. 2009 Jan;37(Database issue):D374-9.
Swelfe is a program that enables you to find internal repeats in DNA sequences, amino-acid sequences or 3D structures.
Swelfe: a detector of internal repeats in sequences and structures.
Bioinformatics. 2008 Jul 1;24(13):1536-7.
TEF is an open-source software for decomposing protein structures into simpler yet informative units named Tightened End Fragments (or closed loops), which can be studied independently to understand protein architecture, folding, and evolution.
TEF2.0: a graph-based method for decomposing protein structures into closed loops.
Distribution of tightened end fragments of globular proteins statistically matches that of topohydrophobic positions: towards an efficient punctuation of protein folding?
Cell Mol Life Sci. 2001 Mar;58(3):492-8.
TuMult is a tool for multiple tumor analysis. TuMult was developed for the analysis of several tumors from the same patient. Using the chromosome breakpoints these tumors have in common, TuMult reconstructs the tumor lineage and the sequence of chromosome aberrations occurring during tumorigenesis. TuMult may be applied to any kind of copy number data.
wwLigCSRre is intended for searching banks for compounds similar to a query, based on both coordinates and physico-chemical properties of atoms.
wwLigCSRre: a 3D ligand-based server for hit identification and optimization.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W504-9.
Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity.
BMC Bioinformatics. 2009 Aug 11;10:245.
Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm.
Comput. Chem. 1998; 22(6):463-5.
Yakusa (Yet Another K-Uples Structure Analyser) is a program devised to rapidly scan a structural database with a query protein structure. It searches for the longest common substructures, called SHSP for "structural high scoring pairs'', between a query structure and every structure in the structural database. It makes use of protein backbone internal coordinates (α angles) in order to describe protein structures as sequences of symbols. It uses a deterministic finite automaton for pattern matching.
YAKUSA: a fast structural database scanning method.
Proteins. 2005 Oct 1;61(1):137-51.