Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins, J Mol Biol, vol.235, pp.983-1002, 1994. ,
Solubility of nonelectrolytes in polar solvents. V. Estimation of the solubility of aliphatic monofunctional compounds in water using a molecular surface area approach, J. Phys ,
Pocketome via comprehensive identification and classification of ligand binding envelopes, Mol. Cell. Proteomics, vol.4, pp.752-761, 2005. ,
Properties of known drugs. 2. Side chains, J. Med ,
The properties of known drugs. 1. Molecular frameworks, J. Med. Chem, vol.39, pp.2887-2893, 1996. ,
Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations, J Med Chem, vol.43, pp.4759-4767, 2000. ,
Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening, J Med Chem, vol.43, pp.2664-2674, 2000. ,
The integrin-actin connection, an eternal love affair, EMBO J, vol.22, pp.2324-2333, 2003. ,
CHARMM: a program for macromolecular energy minimization, and dynamics calculations, J. Comput. Chem, pp.187-217, 1983. ,
Polar hydrogen positions in proteins: empirical energy Conception d'un logiciel de docking et applications dans la recherche de nouvelles molécules actives, p.90 ,
Fragment-Based flexible ligand docking by evolutionary optimization, Biol. Chem, vol.382, pp.1365-72, 2001. ,
Cilengitide targeting of alpha(v)beta(3) integrin receptor synergizes with radioimmunotherapy to increase efficacy and apoptosis in breast cancer xenografts, Cancer Res, vol.62, pp.4263-4272, 2002. ,
Comparative study of several algorithms for flexible ligand docking, J. Comput. Aided. Mol. Des, vol.17, pp.755-63, 2003. ,
Protein docking along smooth association pathways, Proc ,
Ligand atom partial charged assignment for complementary electrostatic potentials, Journal of computer-aided molecular design, vol.6, pp.461-474, 1992. ,
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins, J Med Chem, vol.42, pp.5100-5109, 1999. ,
On evaluating molecular-docking methods for pose prediction and enrichment factors, J. Chem. Inf. Model, vol.46, pp.401-415, 2006. ,
The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals, J. Comput. Chem, vol.26, pp.48-71, 2005. ,
FlexE: efficient molecular Conception d'un logiciel de docking et applications dans la recherche de nouvelles molécules actives, p.90 ,
Comparing protein-ligand docking programs is difficult, Proteins, pp.325-332, 2005. ,
A 'rule of three' for fragment-based lead discovery?, Drug Discov Today, vol.8, pp.876-877, 2003. ,
Coordinate expression of the alpha-6 integrin laminin receptor sub-unit and laminin in breast cancer, J Pathol, vol.165, pp.213-220, 1991. ,
HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site, Proteins, vol.19, pp.199-221, 1994. ,
Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy, J. Med. Chem, vol.47, pp.45-55, 2004. ,
Fragment-based drug discovery ,
Tethering: fragment-based drug discovery, Annu Rev Biophys Biomol Struct, vol.33, pp.199-223, 2004. ,
DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases, J. Comput. Aided. Mol ,
Assessing scoring functions for protein-ligand interactions, J. Med. Chem, vol.47, pp.3032-3079, 2004. ,
Modeling of loops in protein structures, Protein Sci, vol.9, pp.1753-1773, 2000. ,
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy, J. Med ,
SPROUT: recent developments in the de novo design of molecules, J Chem Inf Comput Sci, vol.34, pp.207-217, 1994. ,
A method for localizing ligand binding pockets in protein structures, Proteins, pp.479-488, 2006. ,
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes, J. Mol. Biol, vol.330, pp.891-913, 2003. ,
EADock: docking small molecules into protein active sites with a multiobjective evolutionary optimization, Proteins: structure, function and bioinformatics, vol.67, pp.1010-1025, 2007. ,
Privileged molecules for protein binding identified from NMR-based screening, J Med Chem, vol.43, pp.3443-3447, 2000. ,
A rapid approximation to the solvent accessible surface areas of atoms, Tetrahedron Comput. Methodol, vol.1, pp.103-116, 1988. ,
Signalling via integrins: implications for cell survival and anticancer strategies, Biochim Biophys Acta, vol.1775, pp.163-180, 2007. ,
Ligand efficiency: a useful metric for lead selection, Drug Discov Today, vol.9, pp.430-431, 2004. ,
Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations, J Med Chem, vol.48, pp.5108-5111, 2005. ,
In silico discovery of beta-secretase inhibitors, J Am Chem Soc, vol.128, pp.5436-5443, 2006. ,
Design of small molecule libraries for NMR screening and other applications in drug discovery, Curr Top Med Chem, vol.3, pp.11-23, 2003. ,
Development and validation of a genetic algorithm for flexible docking, J. Mol. Biol, vol.267, pp.727-775, 1997. ,
Screening drug-like compounds by docking to homology models: a systematic study, J. Chem. Inf. Model, vol.46, pp.365-379, 2006. ,
Hit discovery and hit-to-lead approaches, Drug Discov Today, vol.11, pp.741-748, 2006. ,
Docking and scoring in Conception d'un logiciel de docking et applications dans la recherche de nouvelles molécules actives, p.90 ,
Evaluation of docking performance: comparative data on docking algorithms, J Med Chem, vol.47, pp.558-565, 2004. ,
Evaluation of library ranking efficacy in virtual screening, J Comput Chem, vol.26, pp.11-22, 2005. ,
Compressing drug development timelines in oncology using phase '0' trials, Nat Rev Cancer, vol.7, pp.131-139, 2007. ,
X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins, J Mol Biol, vol.259, pp.175-201, 1996. ,
Automated molecular design: a new fragmentjoining algorithm, J Comput Aided Mol Des, vol.8, pp.283-298, 1994. ,
Prediction of Protein-Ligand Interactions. Docking and Scoring: Successes and Gaps, J Med Chem, vol.49, pp.5851-5855, 2006. ,
New analytic approximation to the standard molecular volume definition and its application to generalized born Conception d'un logiciel de docking et applications dans la recherche de nouvelles molécules actives. 83/90 calculations, J. Comput. Chem, vol.24, pp.1348-1356, 2003. ,
Novel generalized Born methods, J. Chem ,
RECAP-retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry, J Chem Inf Comput Sci, vol.38, pp.511-522, 1998. ,
Automated site-directed drug design using molecular lattices, J Mol Graph, vol.10, pp.66-78, 1992. ,
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Advanced Drug Delivery Reviews, vol.46, pp.3-26, 2001. ,
All-atom empirical potential for molecular modeling and dynamics studies of proteins, Journal of Physical Chemistry B, vol.102, pp.3586-3616, 1998. ,
Exhaustive Conception d'un logiciel de docking et applications dans la recherche de nouvelles molécules actives, p.90 ,
Combined simulation and mutagenesis analyses reveal the involvement of key residues for PPARalpha helix 12 dynamic behavior, J Biol Chem, vol.282, pp.9666-9677, 2007. ,
FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known threedimensional structure, J. Comput. Aided. Mol. Des, vol.8, pp.153-174, 1994. ,
Functionality maps of binding sites: a multiple copy simultaneous search method, Proteins, vol.11, pp.29-34, 1991. ,
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function, J. Comput ,
On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites, Proteins, vol.63, pp.892-906, 2006. ,
New aspects of integrin signaling in cancer, Semin Cancer Biol, vol.10, pp.407-414, 2000. ,
PSI-DOCK: Towards highly efficient and accurate flexible ligand docking, Proteins, vol.62, pp.934-946, 2006. ,
Comparative binding energy analysis Conception d'un logiciel de docking et applications dans la recherche de nouvelles molécules actives, p.90 ,
Comments on the Article "On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors, J ,
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance, Proteins, vol.56, pp.235-284, 2004. ,
Interaction with basement membrane serves to rapidly distinguish growth and differentiation pattern of normal and malignant human breast epithelial cells, Proc Natl Acad Sci, vol.89, pp.9064-9068, 1992. ,
A fast flexible docking method using an incremental construction algorithm, J Mol Biol, vol.261, pp.470-489, 1996. ,
Integrins and cell proliferation: regulation of cyclin-dependent kinases via cytoplasmic signaling pathways, J Cell Sci, vol.114, pp.2553-2560, 2001. ,
Free energy simulations come of age: protein-ligand recognition, Acc. Chem. Res, vol.35, pp.430-437, 2002. ,
Structure activity relationship by NMR and by computer: a comparative study, J. Am. Chem. Soc, vol.124, pp.11073-11084, 2002. ,
Protein-ligand docking: current status and future challenges, Proteins, vol.65, pp.15-26, 2006. ,
Semianalytical treatment of solvation for molecular mechanics and dynamics, J. Am. Chem. Soc, vol.112, pp.6127-6129, 1990. ,
Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin, Proteins, vol.40, pp.258-289, 2000. ,
DARWIN: a program for docking flexible molecules, Proteins, vol.41, pp.173-91, 2000. ,
Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding, J Med Chem, vol.49, pp.5880-5884, 2006. ,
Characteristic physical properties and structural fragments of marketed oral drugs, J Med Chem, vol.47, pp.224-232, 2004. ,
A Critical Assessment of Docking Programs and Scoring Functions, J Med Chem, vol.49, pp.5912-5931, 2006. ,
Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites, Chem. Biol, vol.3, pp.449-462, 1996. ,
Multiple functions of the integrin alpha6beta4 in epidermal homeostasis and tumorigenesis, Mol Cell Biol, vol.26, pp.2877-2886, 2006. ,
Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm, J. Comput. Chem, vol.24, pp.1549-62, 2003. ,
Death in the third dimension: apoptosis regulation and tissue architecture, Curr Opin Genet Dev, vol.14, pp.71-80, 2004. ,
Peroxisome proliferator-activated receptor structures: Ligand specificity, molecular switch and interactions with regulators, Biochim Biophys Acta, 2007. ,
Study of the insulin dimerization from binding free energy calculations and per-residue free energy decomposition, Proteins, vol.61, pp.79-93, 2005. ,