SwissParam: A fast force field generation tool for small organic molecules (Q27136894)

ORCID Public Data File 2021

author name string

Vincent Zoete

series ordinal

1

0 references

Michel A. Cuendet

series ordinal

2

0 references

publication date

3 May 2011

0 references

published in

Journal of Computational Chemistry

1 reference

Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics

PubMed

volume

32

0 references

page(s)

2359-2368

0 references

issue

11

0 references

cites work

2 references

21 January 2018

CiteULike CiTO annotations

The Blue Obelisk-interoperability in chemical informatics

2022

1 reference

The many roles of computation in drug discovery

21 January 2018

1 reference

Efficient drug lead discovery and optimization

21 January 2018

1 reference

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

21 January 2018

1 reference

21 January 2018

1 reference

Current topics in computer-aided drug design

21 January 2018

1 reference

Docking, virtual high throughput screening and in silico fragment-based drug design

21 January 2018

1 reference

Towards predictive ligand design with free-energy based computational methods?

21 January 2018

1 reference

Molecular mechanics methods for predicting protein-ligand binding.

21 January 2018

1 reference

Development and testing of a general amber force field

21 January 2018

1 reference

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes

21 January 2018

1 reference

PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules.

21 January 2018

1 reference

Automatic atom type and bond type perception in molecular mechanical calculations

21 January 2018

1 reference

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

21 January 2018

1 reference

CHARMM: the biomolecular simulation program

21 January 2018

1 reference

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

21 January 2018

1 reference

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

21 January 2018

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

21 January 2018

1 reference

The art and practice of structure-based drug design: A molecular modeling perspective

21 January 2018

1 reference

Navigating chemical space for biology and medicine

21 January 2018

1 reference

Trends in virtual combinatorial library design

21 January 2018

1 reference

Virtual screening—an overview

21 January 2018

1 reference

The Cambridge Structural Database: a quarter of a million crystal structures and rising

21 January 2018

1 reference

Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design

21 January 2018

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

21 January 2018

1 reference

UCSF Chimera--a visualization system for exploratory research and analysis

21 January 2018

1 reference

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

21 January 2018

1 reference

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

21 January 2018

1 reference

Ligand-protein database: linking protein-ligand complex structures to binding data

21 January 2018

1 reference

Blind docking of 260 protein-ligand complexes with EADock 2.0.

21 January 2018

1 reference

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

21 January 2018

1 reference

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

21 January 2018

1 reference

FACTS: Fast analytical continuum treatment of solvation.

21 January 2018

1 reference

Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.

21 January 2018

1 reference

Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

21 January 2018

1 reference

Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein–ligand complexes

21 January 2018

1 reference

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

21 January 2018

1 reference

AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB

21 January 2018

1 reference

A semiempirical free energy force field with charge-based desolvation

21 January 2018

1 reference

Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition

21 January 2018

1 reference

Efficient evaluation of binding free energy using continuum electrostatics solvation

21 January 2018

1 reference

In silico discovery of beta-secretase inhibitors.

21 January 2018

1 reference

Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model

21 January 2018

1 reference

Assessing scoring functions for protein-ligand interactions.

21 January 2018

1 reference

Fragment-based lead discovery: leads by design

21 January 2018

1 reference

Knowledge-based scoring function to predict protein-ligand interactions.

21 January 2018

1 reference

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

21 January 2018

1 reference

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

21 January 2018

1 reference

Development and validation of a genetic algorithm for flexible docking

21 January 2018

1 reference

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

21 January 2018

1 reference

Automated docking of flexible ligands: applications of AutoDock

21 January 2018

1 reference

Optimized atomic radii for protein continuum electrostatics solvation forces.

21 January 2018

1 reference

Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring

21 January 2018

1 reference

Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking

21 January 2018

1 reference

The GROMOS Biomolecular Simulation Program Package

21 January 2018

1 reference

Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

21 January 2018

1 reference

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

21 January 2018

1 reference

4 April 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/JCC.21816

Novel generalized Born methods

1 reference

4 April 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/JCC.21816

Chemical space and biology

1 reference

4 April 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/JCC.21816

Identifiers

DOI

10.1002/JCC.21816

1 reference

Consolidated OpenCitations Corpus – April 2017

1594570

DBLP publication ID

journals/jcc/ZoeteCGM11

1 reference

DBLP Dataset 2021-01-02

release_up4i5qxoafcm5d5qqldsbczgte

28 January 2021

Fatcat ID

0 references

1594570

1 reference

Consolidated OpenCitations Corpus – April 2017

Consolidated OpenCitations Corpus – April 2017

1 reference