Journal ArticleDOI
AADS--an automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors
TLDR
A robust automated active site detection, docking, and scoring (AADS) protocol for proteins with known structures that predicts structure and energetics of the complexes agree quite well with experiment when tested on a data set of 170 protein-ligand complexes withknown structures and binding affinities.Abstract:
We report here a robust automated active site detection, docking, and scoring (AADS) protocol for proteins with known structures. The active site finder identifies all cavities in a protein and scores them based on the physicochemical properties of functional groups lining the cavities in the protein. The accuracy realized on 620 proteins with sizes ranging from 100 to 600 amino acids with known drug active sites is 100% when the top ten cavity points are considered. These top ten cavity points identified are then submitted for an automated docking of an input ligand/candidate molecule. The docking protocol uses an all atom energy based Monte Carlo method. Eight low energy docked structures corresponding to different locations and orientations of the candidate molecule are stored at each cavity point giving 80 docked structures overall which are then ranked using an effective free energy function and top five structures are selected. The predicted structure and energetics of the complexes agree quite well...read more
Citations
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Journal ArticleDOI
Latest developments in molecular docking: 2010-2011 in review.
TL;DR: The main developments in docking in this period, covered in this review, are receptor flexibility, solvation, fragment docking, postprocessing, docking into homology models, and docking comparisons.
Journal ArticleDOI
Protein-ligand docking in the new millennium--a retrospective of 10 years in the field
Sérgio F. Sousa,António J. M. Ribeiro,João Coimbra,Rui P. P. Neves,Silvia A. Martins,N.S.H.N. Moorthy,Pedro A. Fernandes,Maria J. Ramos +7 more
TL;DR: Current challenges in the field of protein-ligand docking such as the treatment of protein flexibility, the presence of structural water molecules and its effect in docking, and the entropy of binding are dissected and discussed, trying to anticipate the next years in this field.
Journal ArticleDOI
Sanjeevini: a freely accessible web-server for target directed lead molecule discovery.
Bhyravabhotla Jayaram,Tanya Singh,Goutam Dev Mukherjee,Abhinav Mathur,Shashank Shekhar,Vandana Shekhar +5 more
TL;DR: The article presents Sanjeevini, a freely accessible user friendly web-server, to aid in drug discovery, and describes various modules, their scientific basis, validation, and how to use the server to develop in silico suggestions of lead molecules.
Journal ArticleDOI
A plausible mechanism for the antimalarial activity of artemisinin: A computational approach
TL;DR: Results suggest that artemisinin gets activated by iron which in turn inhibits PfATP6 by closing the phosphorylation, nucleotide binding and actuator domains leading to loss of function of PfATp6 of the parasite and its death.
Journal ArticleDOI
Exoproteome and Secretome Derived Broad Spectrum Novel Drug and Vaccine Candidates in Vibrio cholerae Targeted by Piper betel Derived Compounds
Debmalya Barh,Neha Barve,Krishna Kant Gupta,Sudha Chandra,Neha Jain,Sandeep Tiwari,Nidia León-Sicairos,Adrian Canizalez-Roman,Anderson Rodrigues dos Santos,Syed Shah Hassan,Sintia Almeida,Rommel Thiago Jucá Ramos,Vinicius A. C. Abreu,Adriana Ribeiro Carneiro,Siomar de Castro Soares,Thiago Luiz de Paula Castro,Anderson Miyoshi,Artur Silva,Anil Kumar,Amarendra Narayan Misra,Amarendra Narayan Misra,Kenneth Blum,Kenneth Blum,Eric R. Braverman,Vasco Azevedo +24 more
TL;DR: Preliminary validation suggests that three peptide vaccine candidates that have high potential to induce both B- and T-cell-mediated immune responses from the authors' identified two dual targets are highly effective against Vibrio cholerae.
References
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Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
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Journal ArticleDOI
Development and testing of a general amber force field.
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Journal ArticleDOI
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
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Journal ArticleDOI
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
Garrett M. Morris,David S. Goodsell,Robert Scott Halliday,Ruth Huey,William E. Hart,Richard K. Belew,Arthur J. Olson +6 more
TL;DR: It is shown that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckia genetic algorithm is the most efficient, reliable, and successful of the three.