How do I estimate desolvation energy for protein-ligand complex?

03 March 2016 0 585 Report

I'm trying to estimate differences in binding energies due to differences in desolvation between a set of structurally similar small-molecule inhibitors while docking with a target protein. An online search bring up SeeSAR from BiosolveIT as a software that seems to estimate desolvation energies of a protein-ligand complex. Has anyone used this software? Suggestions about this software or others that can estimate desolvation energies are much appreciated! Thanks in advance for your time and help.

Badges
Science topic

More Sudhir Raghavan's questions See All

Which indexation is better Scopus or Web of Science?

Both are very repetitive indexing agencies.

26 February 2021 9,455 4 View

Anybody write me the name of scopus journals in commerce, management, economics areas. Which publish without any charge?

Please write those scopus journal names for which you have good experience with them.

24 February 2021 6,210 1 View

Do you think NCC and 3 year service at army base must be compulsory to make the students loyal and discipline to the nation?

Decipline and loyalty for nation is the need of today.

09 February 2021 6,928 3 View

What is your opinion regarding opening of school? Now students are supposed to join school. Do you think that decision is in the interest of society ?

From long Pendamic now government is opening school and colleges on for off line classes. What do you think that this decision is fruitful to the students and society too?

08 February 2021 3,068 6 View

What is India's InternationalTrade Policy during Pendamic? How do you find the policy as successful one?

During Covid-19 Pendamic Government are facing problem to maintain business. India is one of them so this question is perfect to be discussed here.

08 February 2021 2,725 3 View

What is the role of IQAC to improve the grading of an institution?

IQAC provides all information about institution and its various activities to NAAC, Bangluru, India in order to get good grading. In this light what is the role of IQAC??

03 February 2021 6,916 1 View

How to measure rod/spindle shaped particle size distribution from FESEM images?

FESEM image showing dense sindle like geometry. Need to measure the particle size distribution.

22 June 2020 3,136 1 View

Can any researcher suggest the relation of NMR and XRD analysis?

need to relate both in my future research

26 April 2020 6,176 3 View

Corona virus testing ?

we have a nano formulation that needs to tested against COVID19. INVITRO in a lab. Does anybody know where it can be tested Dr Ragahvan

31 March 2020 200 9 View

What is the current status of Shallow Gas Exploration in Asian countries?

Shallow Gas exploration can combine conventional exploration (at deeper depths) to exploit small secondary or biogenic pools of hydrocarbon at very low depths in the subsurface. if marketed well,...

17 December 2019 4,374 1 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View