(Q34530633)

2 August 2017

title

Sanjeevini: a freely accessible web-server for target directed lead molecule discovery (English)

1 reference

2 August 2017

0 references

B Jayaram

1

1 reference

2 August 2017

Tanya Singh

2

1 reference

2 August 2017

Goutam Mukherjee

3

1 reference

2 August 2017

Abhinav Mathur

4

1 reference

2 August 2017

Shashank Shekhar

5

1 reference

2 August 2017

Vandana Shekhar

6

1 reference

2 August 2017

publication date

13 December 2012

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2 August 2017

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2 August 2017

volume

13 Suppl 17

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2 August 2017

page(s)

S7

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Creative Commons Attribution 2.0 Generic

2 August 2017

copyright license

start time

1 December 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Lead- and drug-like compounds: the rule-of-five revolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Genomes to hits in silico - a country path today, a highway tomorrow: a case study of chikungunya.

7 July 2018

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In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

The Mycobacterium tuberculosis drugome and its polypharmacological implications

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

An interaction-motif-based scoring function for protein-ligand docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

The cutting edge: membrane-anchored serine protease activities in the pericellular microenvironment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Successful applications of computer aided drug discovery: moving drugs from concept to the clinic

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Automated docking screens: a feasibility study

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

An improved PMF scoring function for universally predicting the interactions of a ligand with protein, DNA, and RNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

From drug target to leads--sketching a physicochemical pathway for lead molecule design in silico

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Computer-aided drug discovery and development (CADDD): in silico-chemico-biological approach

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Development and validation of a modular, extensible docking program: DOCK 5.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

eHiTS: an innovative approach to the docking and scoring function problems.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

MolDock: a new technique for high-accuracy molecular docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Protein Alpha Shape (PAS) Dock: a new gaussian-based score function suitable for docking in homology modelled protein structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Effective handling of induced-fit motion in flexible docking.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Novel procedure for modeling ligand/receptor induced fit effects.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Receptor flexibility in de novo ligand design and docking.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

PatchDock and SymmDock: servers for rigid and symmetric docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

ProPose: steered virtual screening by simultaneous protein-ligand docking and ligand-ligand alignment.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

ZINC--a free database of commercially available compounds for virtual screening

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Docking and scoring in virtual screening for drug discovery: methods and applications

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Development and testing of a general amber force field

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

GEMDOCK: a generic evolutionary method for molecular docking.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Improved protein-ligand docking using GOLD

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Discovery of a novel family of CDK inhibitors with the program LIDAEUS: structural basis for ligand-induced disordering of the activation loop

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Gaussian docking functions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

FlexE: efficient molecular docking considering protein structure variations.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

High throughput docking for library design and library prioritization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Docking ligands onto binding site representations derived from proteins built by homology modelling.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

DoMCoSAR: a novel approach for establishing the docking mode that is consistent with the structure-activity relationship. Application to HIV-1 protease inhibitors and VEGF receptor tyrosine kinase inhibitors.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Molecular modeling and computer aided drug design. Examples of their applications in medicinal chemistry

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

7 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Exhaustive docking of molecular fragments with electrostatic solvation.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

An example of a protein ligand found by database mining: description of the docking method and its verification by a 2.3 A X-ray structure of a thrombin-ligand complex.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Flexible protein-ligand docking by global energy optimization in internal coordinates.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

QXP: powerful, rapid computer algorithms for structure-based drug design.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Modelling protein docking using shape complementarity, electrostatics and biochemical information

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Molecular docking to ensembles of protein structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Molecular docking using surface complementarity.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Flexible ligand docking using a genetic algorithm.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

A multiple-start Monte Carlo docking method.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Rational automatic search method for stable docking models of protein and ligand.

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

FLIPDock: docking flexible ligands into flexible receptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

GAsDock: a new approach for rapid flexible docking based on an improved multi-population genetic algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Modeling water molecules in protein-ligand docking using GOLD.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Pharmacophore-based molecular docking to account for ligand flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

PIPER: an FFT-based protein docking program with pairwise potentials.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

PSI-DOCK: towards highly efficient and accurate flexible ligand docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

SDOCKER: a method utilizing existing X-ray structures to improve docking accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

SODOCK: swarm optimization for highly flexible protein-ligand docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Yucca: an efficient algorithm for small-molecule docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Docking and database screening reveal new classes of Plasmodium falciparum dihydrofolate reductase inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

A swift all-atom energy-based computational protocol to predict DNA-ligand binding affinity and DeltaTm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

Free energy component analysis for drug design: a case study of HIV-1 protease-inhibitor binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

PDBcal: a comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

AADS--an automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

ParDOCK: an all atom energy based Monte Carlo docking protocol for protein-ligand complexes.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Ph4Dock: pharmacophore-based protein-ligand docking

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Fragment-Based flexible ligand docking by evolutionary optimization.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

DARWIN: a program for docking flexible molecules.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

The particle concept: placing discrete water molecules during protein-ligand docking predictions.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3521208

Unsupervised guided docking of covalently bound ligands

27 October 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S17-S7

EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases

21 January 2018

1 reference

12 December 2020

A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets

1 reference

12 December 2020

In silico drug discovery: solving the "target-rich and lead-poor" imbalance using the genome-to-drug-lead paradigm

1 reference

12 December 2020

A molecular thermodynamic view of DNA-drug interactions: a case study of 25 minor-groove binders

1 reference

12 December 2020

Thermodynamic analysis of binding of p-substituted benzamidines to trypsin

1 reference

12 December 2020

MCDOCK: a Monte Carlo simulation approach to the molecular docking problem

1 reference

12 December 2020

Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction

1 reference

12 December 2020

An all atom energy based computational protocol for predicting binding affinities of protein-ligand complexes

1 reference

12 December 2020

The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase

1 reference

12 December 2020

LigScore: a novel scoring function for predicting binding affinities

1 reference

12 December 2020

GlamDock: development and validation of a new docking tool on several thousand protein-ligand complexes

1 reference

12 December 2020

10.1186/1471-2105-13-S17-S7

Identifiers

DOI

1 reference

journals/bmcbi/JayaramSMMSS12

2 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

2 August 2017

1 reference